[gmx-users] Newbie: How to modify the topology file after adding ions?

[Justin A. Lemkul]

Jose Borreguero wrote:
> Hi Justin, thanks for your reply!
> 
> I appended '-p protein.top' to genion. File protein.top was 
> automatically updated by insertion of the following lines at the end of 
> the file:
> /[ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> SOL         7791
> NA+         26
> CL-         23/
> 
> My solvated PDB, protein-solvent.pdb contains lines like these:
> ATOM  24543  NA  NA+  8043      50.712  66.452  12.341  1.00  0.00
> 
> Now when I run grommp, I get the error
> /Fatal error:
> No such moleculetype NA+/
> 
> I checked file gromos45a3.ff/ions.itp. The sodium is included in this 
> fashion:
> /[ moleculetype ]
> ; molname   nrexcl
> NA          1
> [ atoms ]
> ; id    at type res nr  residu name at name  cg nr  charge   mass
> 1       NA+     1       NA          NA             1        22.9898/
> 
> It seems the naming convention of ions.itp is different than that of 
> protein.top and protein-solvent.pdb. I changed protein.top and 

What was your exact genion command?  If you tell genion to use "-pname NA+" 
(which is wrong) you get this result.  Note that the error says the moleculetype 
"NA+" is not found; the moleculetype name is "NA" instead.

> protein-solvent.pdb to match the naming of ions.itp. Then when I run 
> grompp I get the error:
> /ERROR 1 [file protein.top, line 7228]:
>   ERROR: One of the box lengths is smaller than twice the cut-off length.
>   Increase the box size or decrease rlist./
> The puzzling thing is that line 7228 of protein.top is the last line of 
> the file, that is,
> CL      23
> So the error message is not much help :(

The problem comes from the coordinate file and settings of the .mdp file; they 
are somehow incompatible such that they would cause a violation of the minimum 
image convention.  Why the error points to the .top I cannot say.

-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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