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

[Justin A. Lemkul]

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.

-Justin

> Thanks for your time.
> 
> Ricardo.
> 

-- 
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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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