<div>Hi Irene</div>
<div>I've tried to fix the problem ( 2 H atom) using dock prep.</div>
<div>Thanks for your support<br><br></div>
<div class="gmail_quote">2011/4/27 Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hi Elisa,<br>I can't tell from your message what the problem is, so I'm not sure how to solve it.<br>
<br>If the problem is that CHARMM doesn't recognize the atom names and you need to change the names to something else, the simplest approach would probably be to just text-edit the PDB file yourself before using it in CHARMM. You could change atom name with the "setattr" command in Chimera, but text-editing may be easier anyway.<br>
<br>If you just wanted to delete the atoms, you could also do that in Chimera (for example, command: delete :251@1hh1,2hh2) and then use File... Save PDB, but again just text-editing the PDB file may be easier.<br><br>Chimera includes a "Dock Prep" tool for fixing up structures (building missing side chains, etc.; this tool is under Tools... Structure Editing in the menu) and "Write Prmtop" (under Tools... Amber) for generating AMBER input, but it doesn't have anything specifically for CHARMM.<br>
<<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html</a>><br>
<br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D.<br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br>
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<div class="h5"><br>On Apr 27, 2011, at 12:08 PM, elisa carli wrote:<br><br>> Hi,<br>> I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields<br>> Is it possible to fix the problem with Chimera?<br>
> Residues:<br>> ARG 251 1HH1<br>> ARG 251 2HH2<br>> Regards<br><br></div></div></blockquote></div><br>