[gmx-users] Am I wrong ?

David spoel at xray.bmc.uu.se
Sat Nov 30 20:37:45 CET 2002

On Sat, 2002-11-30 at 19:58, Nicolas Michel wrote:
> 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
Most of it sounds OK, only you will have to verify somehow (e.g. testing
energy and density) that the charges can be used with the standard
Lennar Jones parameters.

Genconf is fine, but very crude. You can also just mix the lipids and
water and let it go, after some ns (10-50) you will probably have a nice

> N.
> ----------------------------------------------------
> Nicolas Michel
> Laboratoire de Chimie BioOrganique et des Systemes Moleculaires Vectoriels
> Avignon
> France
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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