[gmx-users] Re: invalid line (coordinates)

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 7 20:34:31 CEST 2011

sarah k wrote:
> dear Justin,
> The link of (http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology)
> helped but still I have problem.
> There are 35344SOL molecules in my _solv.gro file. the last atom is N2
> 72342. The last part of my topol.top file is:
> [molecules]
> ; compound               #mols
> Protein_A                         1
> Protein_B                         1
> Protein_C                         1
> Protein_D                         1
> SOL                          27363
> NA+                                 0
> Then typing grompp commands gives:
> number of coordinates in coordinate file (a_solv.gro, 72342) does not
> match (topol.top, 72341)
> I guess that the topol.top is based on water not matching nitrogen
> that is why I can't balance the numbers.
> I also tried to run again from the begining on my case protein. this
> time I manipulated the topol file with these numbers:
> [molecules]
> ; compound               #mols
> Protein_A                         1
> SOL                          24044
> NA+                                 1
> It started operating but:
> note: System has non-zero total charge: -1.000000e+00 (which is quite logical)
> warning: atom name 210 in topol.top and a_solv.gro does not match (OW- N)
> ......
> WARNING 1 [file topol.top, line 37]: 72133 non matching atom names
> atom names from topol.top will be used
> atom names from a_solv.gro will be ignored
> Does it mean that it will replace the nitrogen solvent with water
> molecules? What should I do this time? Thanks.

If I were you, I'd start over.  Here's why - you've somehow manipulated water 
coordinates and/or topologies to try to make them into nitrogen.  Based on the 
atom naming, it suggests you haven't been very careful in either replacing the 
names, parameters, or both, so you'll end up with a nonsense simulation.

The root of the problem is that you have not properly accounted for the actual 
number of "solvent" molecules you've placed in the system.  Assuming you've 
taken some protein coordinates and used genbox to immerse this structure in 
nitrogen.  The problem here is that genbox understands that "SOL" means water - 
it is hard-coded to do so.  So there may be a problem there.  The solution is to 
use a meaningful name for the nitrogen [moleculetype] (something intuitive and 
distinct like "N2") and correct your topology accordingly.

Without seeing the actual contents of the topologies and all of your commands 
verbatim, there is no way to truly diagnose how you have one stray atom, or even 
if anything in the topology truly applies to your system.


> Best regards,
> Sarah


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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