AMBER Archive (2009)

Subject: Re: [AMBER] Atom names

From: Rose Tamil (rosetamil26_at_googlemail.com)
Date: Wed Jun 03 2009 - 15:43:56 CDT

Hello David,
              Yes, the problem is with the atom names of 2nd residue in PDB.
I solved it with your help. Thanks....
Anitha

On Wed, Jun 3, 2009 at 5:00 PM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Wed, Jun 03, 2009, Rose Tamil wrote:
>
> > I'm trying to get parm and crd files for anthracene stacked
> dimer. I
> > don't have any PDB for that. So i just converted my gaussian output to
> mol2
> > using gauss view and to PDB using Babel.
> > Then, i tried to get the parm and crd files using following
> > commands.
> >
> > source leaprc.ff03
> > loadamberparams gaff.dat
> > loadamberprep PD_prep.prepin
> > com=loadpdb Mol2-PDB.pdb
> > saveamberparm com Mol_Final.parm Mol_Final.crd
> > I'm getting some error saying that "bondAtomProblem found".
>
> Your prepin file lists the residue name as "ANT", but the pdb file has the
> residue name as "LIG". You need to edit the pdb file so that the residue
> name
> matches the one in the prepin file.
>
> Beyond this, the atom names in the second residue in the pdb file are all
> messed up. For example, atoms C9 and C14 are supposed to be bonded to each
> other, but they are 2.8 Ang. apart in the second residue (but OK in the
> first
> residue.)
>
> It looks like you just need to rename the atoms in the PDB file to fix the
> problem.
>
> ...dac
>
>
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