[gmx-users] Fwd: missing atom
ckutzne at gwdg.de
Sat Jul 3 17:50:38 CEST 2010
please keep all Gromacs-related questions on the mailing list.
Begin forwarded message:
> From: "abdul wadood" <wadoodbiochemist at hotmail.com>
> Date: July 3, 2010 8:40:29 AM GMT+02:00
> To: <ckutzne at gwdg.de>
> Subject: missing atom
> Dear Carsten
> I am running simulation using gromacs with amber forcefields on my protein. I have prepared the input file accordingly and have all the required library. But the problem is that when i run pdb2gmx for the top file the following error come:
> WARNING: atom H is missing in residue LEU 2 in the pdb file
> You might need to add atom H to the hydrogen database of residue LEU
> in the file ff???.hdb
> I tried my best to solve the problem, searching on the gromacs website and manual but cannot succeed.
> If you kindly help me in this respect your help will be highly appreciated by our group our research.
> the input file is attached.
> Many regards
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochemist at hotmail.com
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