Thomas Piggot wrote:
Hi,
If I'm not mistaken then I think pdb2gmx is renaming O2 to OXT because
of changes to the entries in the xlateat.dat file (found in the top
folder).
Good point, thanks. I still think it would be a useful improvement if pdb2gmx
double-checked itself. Since that
Hi,
If I'm not mistaken then I think pdb2gmx is renaming O2 to OXT because
of changes to the entries in the xlateat.dat file (found in the top folder).
Cheers
Tom
Justin A. Lemkul wrote:
I have posted a work-around in the discussion of bug #567. I think a code fix
will still be preferable,
I have posted a work-around in the discussion of bug #567. I think a code fix
will still be preferable, ultimately, but if you're stuck, you can give it a try.
http://bugzilla.gromacs.org/show_bug.cgi?id=567
-Justin
Justin A. Lemkul wrote:
Ramachandran G wrote:
Hi Justin,
Presently
Ramachandran G wrote:
Hi Justin,
Presently i too facing the same exact problem. I built the topology
for a chromophore in the protein and entered all the new parameters in
the .rtp, atp, hdb and defined the bonded and nonbonded parameters.
Finally i got the following error.
Fatal error
Hi Justin,
Presently i too facing the same exact problem. I built the topology for
a chromophore in the protein and entered all the new parameters in the .rtp,
atp, hdb and defined the bonded and nonbonded parameters. Finally i got the
following error.
Fatal error:
Atom OXT in residue CRIH 64
Mark Abraham wrote:
- Original Message -
From: "Justin A. Lemkul"
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein us
- Original Message -
From: "Justin A. Lemkul"
Date: Tuesday, September 21, 2010 6:30
Subject: [gmx-users] Problem with pdb2gmx and a new residue
To: Gromacs Users' List
>
> Hi All,
>
> I'm trying to build a topology for a chromophore-containing
> protein using Gromacs 4.5 and OPLS-A
- Original Message - From: "Justin A. Lemkul" Date:
Tuesday, September 21, 2010 6:30 Subject: [gmx-users] Problem with pdb2gmx and
a new residue To: Gromacs Users' List > > Hi All, >
> I'm trying to build a topology for a chromophore-containing > protein using
Gromacs 4.5 and OP
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