[gmx-users] problem with position-restrained dynamics of a charged system

[sebastien santini]

Maybe you have forget to include something (I don't know exactly what)
...
is it possible to post your top and gro files (attached and zipped) ?

it will be easier to find what happened :P .


OZGE ENGIN a écrit :
> Yes, Sebastien! It ends as you wrote. So, it contains info about the number of atoms, and it worked for the previous step. I could not understand the problem :(  
>
>
>
> -----Original Message-----
> From: sebastien santini <santini.s at fsagx.ac.be>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Tue, 22 May 2007 14:27:18 +0100
> Subject: Re: [gmx-users] problem with position-restrained dynamics of a charged system
>
> It seems your topology does not contain any information about number of 
> atoms etc ...
>
> Does your file end with lines like this (for example):
>
> ...
> [ molecules ]
> ; Compound   #mol
> Protein                 1
> NA+                  12
> SOL              1589
>
>
>
> OZGE ENGIN a écrit :
>   
>> Hi all,
>>
>> I have a problem with position-restrained (pr) dynamics of a charged residue in a water box. Up to the position-restrained step, the method worked well; however, it gave the following error in the pr step:
>>
>> Fatal error:
>> number of coordinates in coordinate file (lysine_b4pr.gro, 767)
>>              does not match topology (lysine.top, 0)
>>
>> I could not understand the error because the lysine.top file has already contained the appropriate numbers of atoms defined for protein, ion, and solvent molecules. Moreover, I used the same topology file in the preceding step and it worked. So, what may be the problem?
>>
>> Thanks in advance!
>>
>> Ozge Engin
>>
>>
>>     


-- 
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 Sébastien SANTINI, PhD
 
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