[gmx-users] Coordinate file does not match topology

Yang Ye leafyoung at yahoo.com
Sun Jun 10 14:00:47 CEST 2007


There is 2312-2291=21 more atoms in your structure file than in the 
topology file. If it is due to genion, it shall be less. There might be 
other mistakes in previous steps.

Anyway, to make them match, just count how many molecules you have in 
the system. The last section in your top file shall be something like

[ molecules ]
Protein X
SOL     X
K+      X

Match the number there. Commands like

grep SOL ABC.gro | wc
or
grep Mg ABC.gro | wc
or
grep POT ABC.gro | wc

shall be your good companion.

Regards,
Yang Ye

On 6/10/2007 8:42 AM, Sheyore Omovie wrote:
> Thanks,
> But this is my first real simulation, So I'll appreciate it if you can 
> tell me how to determine the number of ions to add with genion.
> Thanks
> John
>
>
>> From: Alan Dodd <anoddlad at yahoo.com>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Coordinate file does not match topology
>> Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT)
>>
>> Small errors like that are usually down to things like running genion 
>> and not changing the .top.  I think I made a problem for myself once 
>> with non-consecutive atom numbering, too.
>>
>> ----- Original Message ----
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Sent: Friday, June 8, 2007 3:48:28 AM
>> Subject: Re: [gmx-users] Coordinate file does not match topology
>>
>>
>> Sheyore Omovie wrote:
>> > Dear gromacs users,
>> > While trying to preprocess my files with grompp, i got the ff error
>> > message:
>> > "Number of coordinates in coordinate file (b4em.gro, 2312) does not
>> > match topology (twopolypeptide.top, 2291)"
>> > How can I fix this?
>>
>> Make them match. Assuming you haven't managed a gross mismatch of files,
>> your [molecules] section of your .top probably isn't right. Chapter five
>> of the manual is your friend here.
>>
>> Mark
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