<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Francesco,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>As I thought might be the case and mentioned in the previous mail, Amber expects protonated aspartic/glutamic acids to have the proton attached to the other oxygen. What you need to do is simply swap the names of the oxygens in these residues and also change the '1' in the proton name to '2'.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>You were right to break the long bonds, but breaking the bonds turns the formerly connected residues into terminal residues, which means you need an additional oxygen on the 'C' and two additional hydrogens on the 'N'. In addition the hydrogen already attached to 'N' now has the wrong name, since the three hydrogens connected to an N terminus are named H1, H2, and H3, not H. Probably the simplest way to resolve this situation is to run your structure through Dock Prep again (which will fix up the mangled terminii) and write a new PDB file. Also, you will need to delete the unwanted N-terminal 'H' hydrogens before running Dock Prep. You can either just delete them from your input file or use the command 'del :334,223,112,1@H'.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> <BR class="Apple-interchange-newline"> </DIV><BR><DIV><DIV>On Oct 23, 2007, at 10:33 AM, Francesco Pietra wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks to Eric Pettersen I have fixed problems of long bonds and</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">mis-assignement by prepare_amber.pl<SPAN class="Apple-converted-space"> </SPAN>(from HIS to HIE, while it is HID).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Two types of problems remain because I was either unable to correct or did</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">wrongly. The error log from attempted fixing problems:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">WARNING: The unperturbed charge of the unit: 24.000000 is not zero.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 443>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 402>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 386>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 375>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 373>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<NSER 334>.A<H 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 332>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 291>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 275>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 264>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 262>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<NSER 223>.A<H 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 221>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 180>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 164>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 153>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 151>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 128>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<NSER 112>.A<H 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 110>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 69>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 53>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<ASH 42>.A<HD1 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 40>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<GLH 17>.A<HE1 17> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">FATAL:<SPAN class="Apple-converted-space"> </SPAN>Atom .R<NSER 1>.A<H 14> does not have a type.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">UNABLE : I don't know how to rename the hydrogen on serine nitrogen. In my</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">protein.pdb, the section around residues 333/334:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5155<SPAN class="Apple-converted-space"> </SPAN>O <SPAN class="Apple-converted-space"> </SPAN>THR X 333<SPAN class="Apple-converted-space"> </SPAN>15.694 -15.150<SPAN class="Apple-converted-space"> </SPAN>25.132<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>O</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TER<SPAN class="Apple-converted-space"> </SPAN>5156<SPAN class="Apple-converted-space"> </SPAN>THR X 333</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5157<SPAN class="Apple-converted-space"> </SPAN>N <SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-16.176<SPAN class="Apple-converted-space"> </SPAN>22.312<SPAN class="Apple-converted-space"> </SPAN>10.940<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>N</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5158<SPAN class="Apple-converted-space"> </SPAN>H <SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-15.301<SPAN class="Apple-converted-space"> </SPAN>22.760<SPAN class="Apple-converted-space"> </SPAN>10.966<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5159<SPAN class="Apple-converted-space"> </SPAN>CA<SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-16.224<SPAN class="Apple-converted-space"> </SPAN>20.932<SPAN class="Apple-converted-space"> </SPAN>11.429<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>C</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5160<SPAN class="Apple-converted-space"> </SPAN>HA<SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-17.198<SPAN class="Apple-converted-space"> </SPAN>20.770<SPAN class="Apple-converted-space"> </SPAN>11.905<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5161<SPAN class="Apple-converted-space"> </SPAN>CB<SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-15.868<SPAN class="Apple-converted-space"> </SPAN>19.959<SPAN class="Apple-converted-space"> </SPAN>10.306<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>C</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5162<SPAN class="Apple-converted-space"> </SPAN>HB2 SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-15.761<SPAN class="Apple-converted-space"> </SPAN>18.918<SPAN class="Apple-converted-space"> </SPAN>10.709<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5163<SPAN class="Apple-converted-space"> </SPAN>HB3 SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-14.903<SPAN class="Apple-converted-space"> </SPAN>20.280 <SPAN class="Apple-converted-space"> </SPAN>9.956<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5164<SPAN class="Apple-converted-space"> </SPAN>OG<SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-16.906<SPAN class="Apple-converted-space"> </SPAN>19.973 <SPAN class="Apple-converted-space"> </SPAN>9.300<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>O</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5165<SPAN class="Apple-converted-space"> </SPAN>HG<SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-16.948<SPAN class="Apple-converted-space"> </SPAN>20.844 <SPAN class="Apple-converted-space"> </SPAN>8.983<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5166<SPAN class="Apple-converted-space"> </SPAN>C <SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-15.185<SPAN class="Apple-converted-space"> </SPAN>20.856<SPAN class="Apple-converted-space"> </SPAN>12.533<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>C</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>5167<SPAN class="Apple-converted-space"> </SPAN>O <SPAN class="Apple-converted-space"> </SPAN>SER X 334 <SPAN class="Apple-converted-space"> </SPAN>-14.212<SPAN class="Apple-converted-space"> </SPAN>21.643<SPAN class="Apple-converted-space"> </SPAN>12.566<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>O</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Actually, I only inserted "TER" (where it is now) between residue 333 and 334</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to get rid of a long bond between the two; numbering and THR X 333 came out</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">automatically. Also, automatically the pdb file now begins with a series of</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HELIX.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BADLY DONE: to correct for the carboxyl hydrogen being on the wrong oxygen of</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the section</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6851<SPAN class="Apple-converted-space"> </SPAN>CD<SPAN class="Apple-converted-space"> </SPAN>GLU X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.347<SPAN class="Apple-converted-space"> </SPAN>20.009<SPAN class="Apple-converted-space"> </SPAN>21.724<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6852<SPAN class="Apple-converted-space"> </SPAN>OE1 GLU X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.341<SPAN class="Apple-converted-space"> </SPAN>20.227<SPAN class="Apple-converted-space"> </SPAN>23.079<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6853<SPAN class="Apple-converted-space"> </SPAN>OE2 GLU X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.192<SPAN class="Apple-converted-space"> </SPAN>20.919<SPAN class="Apple-converted-space"> </SPAN>20.907<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6854<SPAN class="Apple-converted-space"> </SPAN>HE1 GLU X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.239<SPAN class="Apple-converted-space"> </SPAN>21.145<SPAN class="Apple-converted-space"> </SPAN>23.232<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">was rewritten by exchanging two lines, which automatically were renumbered</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6854<SPAN class="Apple-converted-space"> </SPAN>CD<SPAN class="Apple-converted-space"> </SPAN>GLH X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.347<SPAN class="Apple-converted-space"> </SPAN>20.009<SPAN class="Apple-converted-space"> </SPAN>21.724<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>C</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6855<SPAN class="Apple-converted-space"> </SPAN>OE1 GLH X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.341<SPAN class="Apple-converted-space"> </SPAN>20.227<SPAN class="Apple-converted-space"> </SPAN>23.079<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>O</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6856<SPAN class="Apple-converted-space"> </SPAN>OE2 GLH X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.192<SPAN class="Apple-converted-space"> </SPAN>20.919<SPAN class="Apple-converted-space"> </SPAN>20.907<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>O</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6857<SPAN class="Apple-converted-space"> </SPAN>HE1 GLH X 443 <SPAN class="Apple-converted-space"> </SPAN>-10.239<SPAN class="Apple-converted-space"> </SPAN>21.145<SPAN class="Apple-converted-space"> </SPAN>23.232<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>H</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ATOM <SPAN class="Apple-converted-space"> </SPAN>6858<SPAN class="Apple-converted-space"> </SPAN>C <SPAN class="Apple-converted-space"> </SPAN>GLH X 443 <SPAN class="Apple-converted-space"> </SPAN>-13.205<SPAN class="Apple-converted-space"> </SPAN>16.911<SPAN class="Apple-converted-space"> </SPAN>22.895<SPAN class="Apple-converted-space"> </SPAN>0.00<SPAN class="Apple-converted-space"> </SPAN>0.00 <SPAN class="Apple-converted-space"> </SPAN>C</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and the issue on prepare_amber.pl was not resolved.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">It is obvious that I am carrying out such adjustments for the first time. I got</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the impression that from now on, what I do increases the mess.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Must say that with my imperfect pdb I could carry outt all DOCK tutorials,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">except the amber_score.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">francesco pietra</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">__________________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Do You Yahoo!?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Tired of spam?<SPAN class="Apple-converted-space"> </SPAN>Yahoo! Mail has the best spam protection around<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://mail.yahoo.com">http://mail.yahoo.com</A><SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>