[gmx-users] Problems with GROMPP

[Mark Abraham]

Jens Pohl wrote:
>> -----Ursprüngliche Nachricht-----
>> Von: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Gesendet: 12.01.08 03:29:49
>> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Betreff: Re: [gmx-users] Problems with GROMPP
> 
> 
>>
>>> It seems, that my protein is truncated in the xxx.gro file. The number of water molecules is ok, but there are about 150 AS residues missing after I run GENBOX ??? The xxx.top has them included, so this explains the different numbers.
>> Well, read the warning messages from pdb2gmx, genbox and grompp carefully.
>>
>> Mark
> 
> I didn't receive any warnings going through the single steps. No problem with pdb2gmx. When I compare the *.gro to the original file there seems to be everything ok. Same with editconf. (I rerun pdb3gmx and used -q to get a *.pdb to compare to my original one). When I run genbox I get the *.top with all residues, but the *.gro is truncated. Did it several times with the same result...but no massage, that anything might be wrong (or I was too tired to see it. Will do it again tomorrow)

I'm not sure what the -q output does, but you can select the output 
format simply with the file extension, so pdb2gmx -c out.pdb. I can't 
think of a reason why genbox might truncate a molecule in a structure file.

Mark