From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Nov 01 2011 - 05:59:43 CDT
Jens,
Maybe GUI having predefined fragments make job easier, try for example
with VegaZZ (free) http://www.ddl.unimi.it/. Along with topology
coordinates are also useful (and necessary), so GUI is highly recomendable.
Branko
On 11/1/2011 11:35 AM, Jens K. Munk wrote:
> Dear NAMD-L,
>
> I would like to make a topology file in which lipids are built like peptides, so that each lipid contains eg. four residues, namely:
>
> 1. Head group
> 2. Phosphoglycerol
> 3. Acyl chain on glycerol carbon 2
> 4. Acyl chain on glycerol carbon 3
>
> This would make it much easier to construct any lipid one might be interested in; any combination of acyl chains and head group could be constructed quickly. Also, having defined lipids as made of four residues would make it easier to select eg. chains separately.
>
> I have successfully used this approach to link butanoic acid to phosphoglycerol by defining a BOND between butanoic acid carbon 1 (named C1) and the oxygen on glycerol carbon 2 (named O2), so the BOND definition is
>
> BOND C1 +O2
>
> But I need to be able connect two acyl chains and a head group to the phosphoglycerol. The problem is how to define the connection between eg. two butanoic acid molecules and phosphoglycerol, one at glycerol carbon 2 and the other at glycerol carbon 3 *without* having to define two butanoic acid RESI entries, one for each connection.
>
> My guess is it cannot be done.
>
> Is there any way to pass arguments so that I can choose which oxygen to connect to?
>
> I was thinking about defining the bond at glycerol carbon 2 as above and defining the bond at glycerol carbon 3 as a patch. Very big patch though. Any good?
>
> Later I will define the connection between phosphate and the head group by defining
>
> BOND Cx -O12
>
> where Cx is a head group carbon and O12 is one of the phosphate oxygens.
>
> Any thoughts? TIA.
>
>
>
> --
> Venlig hilsen / Kind Regards
> M. Sc. Jens K. Munk
> Ph.D.-student
> Department of Basic Sciences and the Environment
> KU-LIFE
> Room T432
> Phone +45 3533 2429
> Thorvaldsensvej 40
> DK-1870 Frederiksberg
> Denmark
>
>
>
>
>
>
>
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