[gmx-users] Re: topology error

[lina]

On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA <ithayaraja at gmail.com> wrote:

> only 59 particle variation found out of 230 ligand coordinates.
>
> On 8 October 2011 12:22, ITHAYARAJA <ithayaraja at gmail.com> wrote:
>
>> Dear Sir,
>>
>>
>> I am actually simulating my protein with its ligand so I incorporated all
>> ligand (3) coordinates to my protein .gro file and placed its .itp file
>> also. I used gromas96 43a1 force field.
>>
>> I found following error when i was doing grompp for energy minimization. I
>> went through FAQ and checked all but i couldn't find what exactly it was.
>>
>> So, I attached that files to you. I need your help to solve this
>>
>> Program grompp, VERSION 4.5.1
>> Source code file: grompp.c, line: 377
>>
>> Fatal error:
>> number of coordinates in coordinate file (GR_b4ion.gro, 66074)
>>              does not match topology (GR.top, 66015)
>>
>
I used to count the atom numbers in .gro file and manually modify the
topology to make them match.


>
>>
>> --
>> **
>> Ithayaraja M,
>> Research Scholar,
>> Department of Bionformatics,
>> Bharathiar University,
>> Coimbatore 641 046,
>> Tamil Nadu
>> India
>>
>
>
>
> --
> **
> Ithayaraja M,
> Research Scholar,
> Department of Bionformatics,
> Bharathiar University,
> Coimbatore 641 046,
> Tamil Nadu
> India
>
> --
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