Re: a topology file in VMD

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Apr 25 2007 - 08:58:01 CDT

Hi there,
Since you are going to use charmm topology and parameter files I suggest
first reading the documentation on

http://www.charmm.org/document/Charmm/c32b2/rtop.html
http://www.charmm.org/document/Charmm/c32b2/parmfile.html

DSPC can be built joining two different residues PCGL and STEA and
patches EST1 EST2.
I think there are no parameters for arachidoyl tails so you will have to
develop them.

Topology and parameter files provided with vmd can be found at
vmd/plugins/noarch/tcl/readcharmmpar1.0/par_all27_prot_lipid_na.inp
vmd/plugins/noarch/tcl/readcharmmtop1.0/top_all27_prot_lipid_na.inp

Regards
Cesar

SMAHANE CHALABI escribió:
>
> Dear all,
>
> I have to generate a phospholipid monolayer composed by
> distearoylphosphatidylcholine (DSPC) and
> diarachidoylphosphatidylcholine (DAPC). But these phospholipids are
> not known in VMD version 1.8.6, which is able to generate a
> phospholipid bilayer composed by POPE or POPC as we can see in the
> text consol window such as:
>
> Usage: membrane -l <lipid> -x <xsize> -y <ysize> {-o <prefix>}
> <lipid> is lipid name (POPC or POPE; others as added)
> <xsize> and <ysize> are membrane sizes in X and Y (Angstroms)
> <prefix> is optional output file prefix (default "membrane").
>
> However, I don’t know how to construct the template box structures for
> DAPC and DSPC. I have seen that there is a combined CHARMM
> All-Hydrogen topology file for proteins and lipids, which contains
> POPC and POPE topologies. So, I will certainly have to create a
> topology file for DSPC and DAPC, but I don't know the format of this
> topology file and its exactly localization.
>
> Moreover, is there any way in VMD to construct a phospholipid
> monolayer only and not a bilayer?
>
> Thanks.
>
> Yours sincerely,
> Smahane CHALABI
>
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