[gmx-users] Am I wrong ?

Nicolas Michel n.michel84 at wanadoo.fr
Sat Nov 30 19:58:07 CET 2002

Hi list, sorry for newby's question...
My purpose using gromacs is simulation of nonionic synthetic lipids in water.
Please, before going further (and spend a lot of time in calculations) could you tell me if I'm wrong in any way or any step:
* I build a single molecule of my synthetic lipid by hand, starting with and modifying a "classic" DPPC
* get a "polar H only" pdb file with the Prodrg server (I check the result - it looks good).
* Then I calculate partial charges using 6-31G of Gamess and create an *.itp file with these charges.
* create a *.top file. 
Here, I've got pdb, itp and top files. 
* I transform the pdb into gro with editconf (pdb2gmx don't work with my molecule...), solvate the box with spc216.gro then perform steepest descent and a short md to ensure my system is coherent.
Is this a way to do? do you have suggestion(s)?
Another question, could I use genconf in order to create a bilayer (its syntax is still opaque for me now)?
Thanks in advance


Nicolas Michel
Laboratoire de Chimie BioOrganique et des Systemes Moleculaires Vectoriels
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