VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Dec 02 2009 - 14:03:58 CST

Dear francesco:

I think the procedure to build a rbcg model should be basically the
same as an atomistic one.
1 : obtain the coordinates for your membrane, or protein. This can be
done by coarse graining all-atom model using cgtools plugin.
2 : solvate the system using cgsolvate.tcl
3 : add ions to the system.

About your "cgsolvate.tcl" problem, I think the reason u get the error:
conflicting versions provided for package "solvate": 1.3, then 1.2.
is not because the conflict with VMD 1.8.7, but you already type
"package require solvate" before the command "source ${script_dir}/
cgsolvate.tcl".
Try to open a new fresh VMD console, and type "source ${script_dir}/
cgsolvate.tcl".

But you do need to change the following lines in the cgsolvate.tcl
file to provide correct directory:
   154 readpsf /Projects/anton/ReducedModels/CG/dat/CGSOLV/cgwat.psf
   155 coordpdb /Projects/anton/ReducedModels/CG/dat/CGSOLV/cgwat.pdb
   194 topology /home/amyshih/CGSOLV/water.top

Hope this helps,
Bin

On Dec 2, 2009, at 10:13 AM, Francesco Pietra wrote:

> Hi;
> After I posted the subject problem as secondary matter, I carried out
> an accurate search on the web, unable to find an equilibrated rbcg
> lipid bilayer for vmd 1.8.7/namd martini implementation (or a plain
> procedure to get it from scratch). As for sbcg, I guess that direct
> conversion from an equilibrated all-atoms lipid bilayer will not work.
> Thanks for info.
> francesco pietra