From: Jens K. Munk (jkm_at_life.ku.dk)
Date: Tue Nov 01 2011 - 05:35:37 CDT
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
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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