David, Justin<br><br>Thanks again for help!<br><br><br>I have just few questions about in vacum sumulation of membrane proteins.<br><br><br>I want to simulate GPCR receptor wich have big transmembrane ( helix) domain and some connecting loop regions wich are exposed to the solvent.<br>
<br>As I understood in classical vacum simulation all charges must be redused to avoid its collapse.<br><br>I want to build biphastic system water-vacum-water where loops would be in water and TM helixes in vacum region.<br>
<br>Something like this I've read in old publications about simulation of bacteriorhodopsin <a href="http://ukpmc.ac.uk/abstract/MED/10412722">http://ukpmc.ac.uk/abstract/MED/10412722</a><br><br><br>1- Could you tell me where I could found possible algorithm about builing of such water-vacum-water system?<br>
<br>2- Also I'd like to specify what should I do with the charges residues. I'd like to use AMBER-like or OPLS ff for such simulation As I understood I must neitralize only charges in TM helices and keep residues in LOOP intact. Might this aproache be correct?<br>
<br><br>James<br><br><div class="gmail_quote">2012/1/29 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span><br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="im">On 2012-01-29 17:09, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi, Justin.<br>
<br>
Yes. The GFP chromophore is a part of backbone. It's formed from Ser Tyr<br>
Gly by cyclisation of the Ser with Gly and subsequent dehydrotation. As<br>
the consequence the mature chromophore has cyclised structure wich named<br>
as the CRO residue in PDB structure.<br>
<br>
I've made for this CRO residue topology via PRODG server for GROMOS ff.<br>
<br>
Than I've imported that new chromophore.top into the topology.top of my<br>
structure in accordance to your tutorial.<br>
<br>
Finally I've merged CRO.gro and protein.gro ( I've cut CRO from the pdb<br>
for creation of the topoogy for my protein via pdb2gmx)<br>
<br>
Than I've done minimisation and chromophore have been diffused from my<br>
protein :) It seems that I must add covalent bond between CRO and<br>
protein into the topology. But how I could do it for my multi topology<br>
file ?<br>
</blockquote>
<br></div>
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.<br>
<br>
Of course you can make all the bonds, angles, diehdrals and pairs manually as well, but that is tedious and error prone.<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
James<br>
<br>
2012/1/29 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div class="h5"><br>
<br>
<br>
<br>
James Starlight wrote:<br>
<br>
Hi David!<br>
<br>
Thanks for reference I'll study it carefully.<br>
<br>
<br>
I have some general question about the vacuum simulation<br>
<br>
1- I've found that common GROMOS fields are not suitable for the<br>
vacuum simulation because of its implementation for condensed<br>
phase .<br>
But In some referencces I've found that people use 53.6 ff for<br>
the in<br>
vacuum simulation. In addition Ive done minimisation and<br>
equilibration<br>
in that ff in vacuum and my system have not been collapse :) Is<br>
there<br>
any wy to adopt this ff for the in vacum ?<br>
<br>
2- I have uncommon onject for simulation. It's GFP protein where<br>
chromophore group ( like ligand) is covalent bonded to the<br>
backbone of<br>
this protein. As I've understood in Justins tutorial there are<br>
no any<br>
covalent bonds between protein and ligand. But how I could make this<br>
bond if I operate with TWO topology files ( one for chromophore and<br>
another for protein itself) ? I've done all steps in accordance to<br>
Justins tutorial but on the minimisation step my chromphore dissuse<br>
out of the protein interior because of absent of backbone group.<br>
<br>
<br>
The GFP chromophore is part of the backbone of the protein, is it not?<br>
<br>
The tutorial I have for a protein-ligand complex should not be taken<br>
to mean that all non-protein entities are physically separate<br>
entities. Plenty of cofactors, chromophores, and the like are<br>
covalently attached to the protein.<br>
<br>
-Justin<br>
<br>
--<br></div></div>
==============================<u></u>__==========<div class="im"><br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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</blockquote><div class="im HOEnZb">
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