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

[Jose Borreguero]

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
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 :(

-Jose

On Wed, Dec 7, 2011 at 11:04 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jose Borreguero wrote:
>
>> Dear Gromacs users,
>>
>> Im new to gromacs and I'm following a tutorial (http://nmr.chem.uu.nl/~**
>> tsjerk/course/molmod/ <http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/>).
>> Unfortunately, the tutorials doesn't say anything about how to update the
>> topology file after using 'genion' to replace a few water molecules with
>> ions.
>> I manually edited the topology file and updated the number of water
>> molecules and added the number of ions:
>>
>>
> Using the -p flag will make all the necessary changes automatically.
>
>
>  [ molecules ]
>> ; Compound        #mols
>> Protein_chain_A     1
>> SOL              7791
>> Na+              26
>> Cl-              23
>>
>> But then when I tried to preprocess the structure with grompp, I got an
>> error:
>>
>> Fatal error:
>> No such moleculetype Na+
>>
>>
> Assuming you're using a new version of Gromacs (4.5.x), the naming scheme
> has changed.  Check the ions.itp for the force field you've chosen to use
> to set proper names.
>
> -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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