[gmx-users] including a new molecule to forcefield

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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