[gmx-users] Re: grompp error- Excluding 3 bonded neighbours-Fatal error

[sanjay23 at iitb.ac.in]

> dear dean,
there is no problem with your mdp file. for grompp number of atoms in .top
file and input .gro file should be equal,look your.top file, this may be
because u have added number of ions in your .top file but it not present
in your .gro file( difference of 8 atom only in both file, which equal to
no of ions u have to aded for nutrilizing your system). look both file and
try to manage.
sanjay

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> Today's Topics:
>
>    1. Re: Problem with adding H using amber03 (Justin A. Lemkul)
>    2. NVT or NPT ? (Chih-Ying Lin)
>    3. NVT or NPT ? (chris.neale at utoronto.ca)
>    4. RE: anomalous free energy dgdl.xvg values every nstlist	steps
>       while using a twin-range cutoff (Berk Hess)
>    5. grompp error- Excluding 3 bonded neighbours-Fatal error
>       (Dean Cuebas)
>    6. Re: NVT or NPT ? (Tsjerk Wassenaar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 17 Feb 2009 20:43:09 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Problem with adding H using amber03
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <499B67AD.9010506 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Peggy Yao wrote:
>> Dear all,
>>
>> I am trying to use amber03 force field. I corrected the amino acid names
>> as described on http://chemistry.csulb.edu/ffamber/.
>>
>> However, when I ran pdb2gmx on a PDB file without H-atoms, I got the
>> following error:
>>
>> pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb
>>
>> ...
>> WARNING: atom H is missing in residue THR 1 in the pdb file
>>          You might need to add atom H to the hydrogen database of
>> residue THR
>>          in the file ff???.hdb (see the manual)
>>
>
> Obviously you did not follow all of the directions.  If Thr is amino acid
> 1
> (i.e., the N-terminus) it should be called NTHR.
>
> -Justin
>
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.0.2
>> Source code file: pdb2top.c, line: 701
>>
>>%2