[gmx-users] Problem on solvating system with non-water solvent

[Justin Lemkul]

On 4/1/19 8:32 AM, Tingguang.S wrote:
> Dear All,
>
>
> I had creating a box with 100 formic acid molecules in it, and copied the gro file of the box into the Gramacs topology directory after minimization and equilibration steps. The sovation step  with this formic acid box succeeded, but the next step is not OK when using the command line: gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr,  the error code is: ERROR 1 [file topol.top, line 3772]:  No such moleculetype FORH.  FORH is the exiting entry in the rtp file. Does it mean that I need create an itp file for the fomic acid box ? Thank you for your suggestion!

The .rtp files are only ever used by pdb2gmx. You need an .itp file that 
defines the solvent, just like you would with water or anything else.

-Justin

>
>
>
> My topology file looks like this:
>
>
> ; Include forcefield parameters
> #include "charmm36-nov2018.ff/forcefield.itp"
>
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_chain_A     3
>
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
> ; residue   1 THR rtp THR  q +1.0
>       1        NH3      1    THR      N      1       -0.3     14.007
>       2         HC      1    THR     H1      2       0.33      1.008
>       3         HC      1    THR     H2      3       0.33      1.008
>       4         HC      1    THR     H3      4       0.33      1.008
>     .................................................................................
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
>
> [ system ]
> ; Name
> Protein in water
>
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> FORH             1773
>
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-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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