[gmx-users] Coordinate file does not match topology

[Yang Ye]

There is 2312-2291=3D21 more atoms in your structure file than in the=20
topology file. If it is due to genion, it shall be less. There might be=20
other mistakes in previous steps.

Anyway, to make them match, just count how many molecules you have in=20
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=20
> 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=20
>> and not changing the .top.  I think I made a problem for myself once=20
>> 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 file=
s,
>> your [molecules] section of your .top probably isn't right. Chapter fi=
ve
>> of the manual is your friend here.
>>
>> Mark
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