[gmx-users] Problem on solvating system with non-water solvent
Justin Lemkul
jalemkul at vt.edu
Tue Apr 9 17:34:02 CEST 2019
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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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
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