[gmx-users] Fwd: missing atom

Carsten Kutzner ckutzne at gwdg.de
Sat Jul 3 17:50:38 CEST 2010

Dear Abdul,

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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