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
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
3. Run pdb2gmx to obtain a single topology
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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