a topology file in VMD

From: SMAHANE CHALABI (smahane_chalabi_at_hotmail.com)
Date: Wed Apr 25 2007 - 02:57:42 CDT

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?


Yours sincerely,

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