[gmx-users] different number of waters (grompp)

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> Ricardo O. S. Soares wrote:
>> Hello dear users,
>>
>> I'm having a problem trying to simulate one trimer. I'm using tip4p 
>> water and right after I fill the box with water and try to pre-process 
>> (grompp) the resulting .gro and .top, I get the following error:
>>
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 4.5.1
>> Source code file: grompp.c, line: 377
>>
>> Fatal error:
>> number of coordinates in coordinate file (../box/box_water.gro, 274045)
>>              does not match topology (../top_water.top, 273029)
>> For more information and tips for troubleshooting, please check the 
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>> Here's the ending of the .top file:
>>
>> [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> Protein_chain_H     1
>> Protein_chain_L     1
>> SOL                59
>> SOL                97
>> SOL                98
>> SOL             66032
>>
>> And the beginning of the .gro file shows the number "274045"
>>
> 
> The .top specifies fewer atoms than the .gro, so it's possible that 
> there was some problem when genbox wrote the topology.  The screen 
> output of genbox should have indicated how many waters were added - does 
> this number match what you see in the .top?  Presumably the first three 
> SOL entries are crystal waters?  I don't know that pre-existing waters 
> should cause any problem, but it's possible.  The difference in the 
> number of atoms is 1016, or 254 TIP4P molecules. Coincidentally, 59 + 97 
> + 98 = 254.  It looks like genbox wrote the wrong number  of molecules 
> it added.  If this is the case, please file an issue on 
> redmine.gromacs.org with the exact steps taken to reproduce the problem 
> so it can be fixed.
> 

I just noticed you're using version 4.5.1, so you should upgrade to 4.5.4 and 
see if the issue persists before filing any report.  Debugging outdated versions 
which may have already been fixed is not terribly productive :)

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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