[gmx-users] including a new molecule to forcefield
jalemkul at vt.edu
Sun May 5 02:30:51 CEST 2013
On 5/4/13 8:28 PM, Amir Abbasi wrote:
> Hi All,
> I want to simulate graphene oxide in water. i have used swissparam server to create .itp file of it.
> then i'd put the .itp file in oplsaa.ff folder and edit forcefield.itp file and insert:
> #include "GRO.itp"
Do not edit forcefield.itp in this way.
> but when i want to use pdb2gmx to make topology file,it says:
> Residue 'GRO' not found in residue topology database
> what should i do?
Don't run pdb2gmx on the structure. The job of pdb2gmx is to produce a
topology, which you already have. All you have to do is #include "GRO.itp" in
your system's .top file. Leave the other files in your force field folder alone.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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