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

[Jose Borreguero]

This tutorial doesn't seem to be quite useful, if so many errors pop up.
Maybe it was implemented for Gromacs < 4.5.x but there's no info on the
version it should be used.

However, Lo and behold! I found that you have a nice page with Gromacs
4.5.x tutorials :D  (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
I'll give a try with the Lyzosyme one!

- Jose

On Wed, Dec 7, 2011 at 1:29 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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