[Chimera-users] Information request

[elisa carli]

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 at 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 at 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
>
>
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