[gmx-users] Force Field for Vacuum simulation

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 29 17:50:52 CET 2012

On 2012-01-29 17:09, 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.
> 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)
> 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 need to add the bonds angles etc. The easiest way would be to make a 
special bond (specbond.dat file). You need an rtp entry for your cro 
group as well. Then pdb2gmx makes the necessary bonds.

Of course you can make all the bonds, angles, diehdrals and pairs 
manually as well, but that is tedious and error prone.
> James
> 2012/1/29 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     James Starlight wrote:
>         Hi David!
>         Thanks for reference I'll study it carefully.
>         I have some general question about the vacuum simulation
>         1- I've found that common GROMOS fields are not suitable for the
>         vacuum simulation because of its implementation for condensed
>         phase .
>         But In some referencces I've found that people use 53.6 ff for
>         the in
>         vacuum simulation. In addition Ive done minimisation and
>         equilibration
>         in that ff in vacuum and my system have not been collapse :) Is
>         there
>         any wy to adopt this ff for the in vacum ?
>         2- I have uncommon onject for simulation. It's GFP protein where
>         chromophore group ( like ligand) is covalent bonded to the
>         backbone of
>         this protein. As I've understood in Justins tutorial there are
>         no any
>         covalent bonds between protein and ligand. But how I could make this
>         bond if I operate with TWO topology files ( one for chromophore and
>         another for protein itself) ? I've done all steps in accordance to
>         Justins tutorial but on the minimisation step my chromphore dissuse
>         out of the protein interior because of absent of backbone group.
>     The GFP chromophore is part of the backbone of the protein, is it not?
>     The tutorial I have for a protein-ligand complex should not be taken
>     to mean that all non-protein entities are physically separate
>     entities.  Plenty of cofactors, chromophores, and the like are
>     covalently attached to the protein.
>     -Justin
>     --
>     ==============================__==========
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>     ==============================__==========
>     --
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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