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

[sebastien santini]

Your topology file contains

SOL    2490

and your coordinate file only 249 water molecules

change 2490 to 249 in the top file and see what happens.


OZGE ENGIN a écrit :
> Thank you very much for your attention :) I attached the needed gro and top files. 
>
>
> -----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 14:52:13 +0100
> Subject: Re: [gmx-users] problem with position-restrained dynamics of a	charged system
>
> 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
 
 http://sebastien.santini.free.fr
 
 CBMN, Faculté Universitaire des Sciences Agronomiques  
 Passage des déportés, 2  
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