problems with CG protein-lipidbilayer-water system

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Nov 21 2009 - 12:00:54 CST

Hi:
I have already posted fragments in the Subject topic. I got some
important advice but I am still in the open sea. Therefore, I
summarize the status, in the hope to get further input. I am aimed at
setting up a transmembrane protein in a POPC, DOPC (or other common
polar lipid) bilayer, and water solvated, coarse-grained system. I
followed Anton's advice (mail archives) to coarse gain separately the
components rather than the whole system.

I first tried - as an assay - to cg solvate the protein using the files that
Anton has put on the web <http://www.ks.uiuc.edu/Research/CG/rbcg/files/>

cgionize.tcl 20-Nov-2009 12:01 8k
[ ] cgsolvate.tcl 31-Aug-2009 20:19 20k
[ ] cgwat.pdb 31-Aug-2009 20:19 42k
[TXT] cgwat.psf 31-Aug-2009 20:19 44k
[TXT] dopc.cgc 31-Aug-2009 20:19 2k
[TXT] lipid.cgc 31-Aug-2009 20:19 2k
[TXT] rbcg-2007.par 31-Aug-2009 20:19 24k
[TXT] rbcg-2007.top 31-Aug-2009 20:19 8k

If cgsolvate.tcl is added to

/usr/local/lib/vmd/plugins/noarch/tcl/solvate1.3

it is not seen by the command

package require ...

Then I put cgsolvate.tcl in my working directory. Command

source cgsolvate.tcl

reported

conflicting versions provided for package "solvate": 1.3, then 1.2.

My first question is: should I downgrade to VMD 1.8.6? Anton's files
are not that old, 31 AUG 2009.

My second question: are the above files for lipids enough for my task?

My third question: at present is it still advisable to coarse grain
the components rather that the all-atom final system using the auto cg
builder?

Thanks for answering

francesco pietra

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