[Chimera-users] Atom does not have a type
Eric Pettersen
pett at cgl.ucsf.edu
Wed Oct 24 16:41:15 PDT 2007
Hi Francesco,
You can probably send further replies directly to me or Elaine since
this is getting pretty detailed and is probably not of much interest
to the rest of the list.
On Oct 24, 2007, at 2:29 AM, Francesco Pietra wrote:
> Hi Eric:
> I do believe things are now rightly channeled. Though, there are
> messages that
> I do not understand. To this concern, which part of the chimera
> guidelines
> should be mastered, if not all parts?
>
> I started again (with Chimera 17 Oct daily build) from the non-
> standard-pdb
> protein model that you had in large part fixed.
I have now put in further fixes for some of the situations found in
your files. You should get the October 24th build and use that
(available about 6 hours from now).
> I did in this sequence:
>
> (1) Deleting the single HOH molecule still present deep into the pore.
>
> (2) Replacing HIS with HID (as HID was evident from Chimera graphics).
>
> (3) Replacing ASP and GLU with ASH and GLH, respectively. In
> addition, swapping
> the names for the oxygens and changing "1" to "2" in the proton
> name for both
> ASH and GLH.
Also, some of these residues are carboxylates rather than carboxylic
acids. You should leave the carboxylate residue names as ASP/GLU.
> (4) Insert "TER" (columns 1-3) to get rid of long bonds.
>
> (5) From command line del:#,#,#,1 at H
>
> (6) Running Dock-Prep (all selected, except "Delete non-complexed
> ions"; also
> consider H-bonds; residue name HID specified.
> A query was presented (in SYBYL naming) that I did not find where
> to get help
> about; therefore, I accepted the charge settings as it was presented:
>
> ASH + ALA + ASN +0
>
> ASH + ALA + PRO +0
>
> ASH + GLY + MET +0
>
> GLH + ARG + LEU (w/HE2-1) +1
>
> GLH + ARG + LEU (wo/HE2-1) +0
>
> GLH + ARG + THR (w/1H-3) (wo/OXT-3) +1
>
> GLH + ARG + THR (w/OXT-3) (wo/1H-3) +0
Will not happen with the October 24 build.
--Eric
> On saving mol2, 1 model(s) had non-integral charge. I loaded this
> mol2 file to
> Chimera and saved as pdb.
>
> As to the non-integrals, from the log file:
> The following residues had non-integral charges:
> ARG 16.X 0.959956
> GLH 17.X -0.000762712
> LEU 18.X 0.0411068
> ALA 39.X 0.0239333
> GLH 40.X -0.00136667
> ALA 41.X -0.0225667
> ASH 42.X -0.0299946
> ASN 43.X 0.0290135
> PRO 52.X -0.00862973
> ASH 53.X -0.0208919
> ALA 54.X 0.0297216
> GLY 68.X 0.00385946
> ASH 69.X -0.0233324
> MET 70.X 0.019273
> ARG 109.X 0.99236
> GLH 110.X 0.03004
> THR 111.X -0.0223
> ARG 127.X 0.959956
> GLH 128.X -0.000762712
> LEU 129.X 0.0411068
> ALA 150.X 0.0239333
> GLH 151.X -0.00136667
> ALA 152.X -0.0225667
> ASH 153.X -0.0299946
> ASN 154.X 0.0290135
> PRO 163.X -0.00862973
> ASH 164.X -0.0208919
> ALA 165.X 0.0297216
> GLY 179.X 0.00385946
> ASH 180.X -0.0233324
> MET 181.X 0.019273
> ARG 220.X 0.99236
> GLH 221.X 0.03004
> THR 222.X -0.0223
> ARG 238.X 0.921552
> GLH 239.X -0.870055
> LEU 240.X -0.0509966
> ALA 261.X 0.0239333
> GLH 262.X -0.00136667
> ALA 263.X -0.0225667
> ASH 264.X -0.0299946
> ASN 265.X 0.0290135
> PRO 274.X -0.00862973
> ASH 275.X -0.0208919
> ALA 276.X 0.0297216
> GLY 290.X 0.00385946
> ASH 291.X -0.0233324
> MET 292.X 0.019273
> ARG 331.X 0.99236
> GLH 332.X 0.03004
> THR 333.X -0.0223
> ARG 349.X 0.921552
> GLH 350.X -0.870055
> LEU 351.X -0.0509966
> ALA 372.X 0.0239333
> GLH 373.X -0.00136667
> ALA 374.X -0.0225667
> ASH 375.X -0.0299946
> ASN 376.X 0.0290135
> PRO 385.X -0.00862973
> ASH 386.X -0.0208919
> ALA 387.X 0.0297216
> GLY 401.X 0.00385946
> ASH 402.X -0.0233324
> MET 403.X 0.019273
> ARG 442.X 0.990084
> GLH 443.X -0.00581091
> THR 444.X -0.984373
> 1 model(s) had non-integral total charge.
>
> I examined on Chimera the THR 444.X. It is terminal, thus OK -1
> charge (on OXT
> carboxylate oxygen). This THR on the saved pbd reads as follows:
> HETATM 6894 O GLH X 443 -14.087 17.680 23.309 1.00
> 0.00 O
> ATOM 6895 N THR X 444 -13.468 15.692 22.402 1.00
> 0.00 N
> ATOM 6896 H THR X 444 -12.701 15.104 22.036 1.00
> 0.00 H
> ATOM 6897 CA THR X 444 -14.614 14.887 22.695 1.00
> 0.00 C
> ATOM 6898 HA THR X 444 -15.533 15.302 22.270 1.00
> 0.00 H
> ATOM 6899 CB THR X 444 -14.455 13.483 21.996 1.00
> 0.00 C
> ATOM 6900 HB THR X 444 -15.409 12.889 22.079 1.00
> 0.00 H
> ATOM 6901 CG2 THR X 444 -14.392 13.621 20.466 1.00
> 0.00 C
> ATOM 6902 1HG2 THR X 444 -14.437 12.695 19.945 1.00
> 0.00 H
> ATOM 6903 2HG2 THR X 444 -15.193 14.291 20.199 1.00
> 0.00 H
> ATOM 6904 3HG2 THR X 444 -13.474 14.106 20.129 1.00
> 0.00 H
> ATOM 6905 OG1 THR X 444 -13.355 12.751 22.443 1.00
> 0.00 O
> ATOM 6906 HG1 THR X 444 -12.543 13.311 22.233 1.00
> 0.00 H
> ATOM 6907 C THR X 444 -14.809 14.814 24.227 1.00
> 0.00 C
> ATOM 6908 O THR X 444 -15.798 15.199 24.830 1.00
> 0.00 O
> ATOM 6909 OXT THR X 444 -13.895 14.330 24.891 1.00
> 0.00 O
> CONECT 255 258 256 236
>
> I did nothing more (planned flex docking and amber_score with
> DOCK). I'll wait
> until the above is approved or rejected. (I was unable to command the
> visualization in Chimera of a particular residue, say THR 444.
> Command :THR:444
> returned all THR.
>
> Thanks
>
> francesco
>
>
>
>
>
>
> --- Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> Hi Francesco,
>> 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'.
>> 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 at H'.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>> pett at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu
>>
>>
>> On Oct 23, 2007, at 10:33 AM, Francesco Pietra wrote:
>>
>>> Thanks to Eric Pettersen I have fixed problems of long bonds and
>>> mis-assignement by prepare_amber.pl (from HIS to HIE, while it is
>>> HID).
>>>
>>> Two types of problems remain because I was either unable to correct
>>> or did
>>> wrongly. The error log from attempted fixing problems:
>>> WARNING: The unperturbed charge of the unit: 24.000000 is not zero.
>>> FATAL: Atom .R<GLH 443>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<ASH 402>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 386>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 375>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<GLH 373>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<NSER 334>.A<H 14> does not have a type.
>>> FATAL: Atom .R<GLH 332>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<ASH 291>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 275>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 264>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<GLH 262>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<NSER 223>.A<H 14> does not have a type.
>>> FATAL: Atom .R<GLH 221>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<ASH 180>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 164>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 153>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<GLH 151>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<GLH 128>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<NSER 112>.A<H 14> does not have a type.
>>> FATAL: Atom .R<GLH 110>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<ASH 69>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 53>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<ASH 42>.A<HD1 14> does not have a type.
>>> FATAL: Atom .R<GLH 40>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<GLH 17>.A<HE1 17> does not have a type.
>>> FATAL: Atom .R<NSER 1>.A<H 14> does not have a type.
>>>
>>> UNABLE : I don't know how to rename the hydrogen on serine
>>> nitrogen. In my
>>> protein.pdb, the section around residues 333/334:
>>>
>>> ATOM 5155 O THR X 333 15.694 -15.150 25.132 0.00
>>> 0.00 O
>>> TER 5156 THR X 333
>>> ATOM 5157 N SER X 334 -16.176 22.312 10.940 0.00
>>> 0.00 N
>>> ATOM 5158 H SER X 334 -15.301 22.760 10.966 0.00
>>> 0.00 H
>>> ATOM 5159 CA SER X 334 -16.224 20.932 11.429 0.00
>>> 0.00 C
>>> ATOM 5160 HA SER X 334 -17.198 20.770 11.905 0.00
>>> 0.00 H
>>> ATOM 5161 CB SER X 334 -15.868 19.959 10.306 0.00
>>> 0.00 C
>>> ATOM 5162 HB2 SER X 334 -15.761 18.918 10.709 0.00
>>> 0.00 H
>>> ATOM 5163 HB3 SER X 334 -14.903 20.280 9.956 0.00
>>> 0.00 H
>>> ATOM 5164 OG SER X 334 -16.906 19.973 9.300 0.00
>>> 0.00 O
>>> ATOM 5165 HG SER X 334 -16.948 20.844 8.983 0.00
>>> 0.00 H
>>> ATOM 5166 C SER X 334 -15.185 20.856 12.533 0.00
>>> 0.00 C
>>> ATOM 5167 O SER X 334 -14.212 21.643 12.566 0.00
>>> 0.00 O
>>>
>>> Actually, I only inserted "TER" (where it is now) between residue
>>> 333 and 334
>>> to get rid of a long bond between the two; numbering and THR X 333
>>> came out
>>> automatically. Also, automatically the pdb file now begins with a
>>> series of
>>> HELIX.
>>>
>>> BADLY DONE: to correct for the carboxyl hydrogen being on the wrong
>>> oxygen of
>>> ASP (renamed ASH) and GLU (renamed GLH), for example, for 443 the
>>> section
>>>
>>> ATOM 6851 CD GLU X 443 -10.347 20.009 21.724 0.00 0.00
>>> ATOM 6852 OE1 GLU X 443 -10.341 20.227 23.079 0.00 0.00
>>> ATOM 6853 OE2 GLU X 443 -10.192 20.919 20.907 0.00 0.00
>>> ATOM 6854 HE1 GLU X 443 -10.239 21.145 23.232 0.00 0.00
>>>
>>> was rewritten by exchanging two lines, which automatically were
>>> renumbered
>>>
>>> ATOM 6854 CD GLH X 443 -10.347 20.009 21.724 0.00
>>> 0.00 C
>>> ATOM 6855 OE1 GLH X 443 -10.341 20.227 23.079 0.00
>>> 0.00 O
>>> ATOM 6856 OE2 GLH X 443 -10.192 20.919 20.907 0.00
>>> 0.00 O
>>> ATOM 6857 HE1 GLH X 443 -10.239 21.145 23.232 0.00
>>> 0.00 H
>>> ATOM 6858 C GLH X 443 -13.205 16.911 22.895 0.00
>>> 0.00 C
>>>
>>> and the issue on prepare_amber.pl was not resolved.
>>>
>>> It is obvious that I am carrying out such adjustments for the first
>>> time. I got
>>> the impression that from now on, what I do increases the mess.
>>>
>>> Must say that with my imperfect pdb I could carry outt all DOCK
>>> tutorials,
>>> except the amber_score.
>>>
>>> Thanks
>>> francesco pietra
>>>
>>>
>>>
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>>
>>
>
>
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