[gmx-users] Force Field for Vacuum simulation

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 29 17:47:33 CET 2012

James Starlight wrote:
> Hi, Justin.
> Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr 
> Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As 
> the consequence the mature chromophore has cyclised structure wich named 
> as the CRO residue in PDB structure.
> I've made for this CRO residue topology via PRODG server for GROMOS ff.
> Than I've imported that new chromophore.top into the topology.top of my 
> structure in accordance to your tutorial.

This is the wrong approach.  The chromophore is not a separate ligand, but 
rather a constituent part of the protein.  You need to treat it as such.

> Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the pdb 
> for creation of the topoogy for my protein via pdb2gmx)

Certainly this left a massive gap in the protein backbone and likely you got 
long bond warnings.

> Than I've done minimisation and chromophore have been diffused from my 
> protein :) It seems that I must add covalent bond between CRO and 
> protein into the topology. But how I could do it for my multi topology 
> file ?

You cannot. Bonds can only be created within a single [moleculetype] and thus 
multiple topologies cannot be used here.  The proper procedure would be:

1. Derive parameters for the chromophore (PRODRG is a bad choice), or use those 
already present in the literature (they exist for CHARMM27, and perhaps others, 
as people have been simulating GFP for years).
2. Follow the instructions at 
3. Run pdb2gmx to obtain a single topology



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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