Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards
Hi Elisa, I can't tell from your message what the problem is, so I'm not sure how to solve it. 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. 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. 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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 27, 2011, at 12:08 PM, elisa carli wrote:
Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards
Hi Irene I've tried to fix the problem ( 2 H atom) using dock prep. Thanks for your support 2011/4/27 Elaine Meng <meng@cgl.ucsf.edu>
Hi Elisa, I can't tell from your message what the problem is, so I'm not sure how to solve it.
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.
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.
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. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.h...
< http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 27, 2011, at 12:08 PM, elisa carli wrote:
Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards
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