TM protein in octane slab questions

From: Michel Seigneuret (
Date: Fri Jul 22 2005 - 03:52:50 CDT

Dear Namd users,
I would like to do some MD on a transmembrane protein with Namd
using an octane slab with water (due to limited computational resources).
Here are a few questions:
1) While there are many publications doing this with full phospholipids
using either Namd or Gromacs, most publications with octane use Gromacs
( I found only one octane work with Namd). Is there a reason why Gromacs
should be better for octane slabs ? I would prefer to use Namd since I have
(limited) experience with it.
2) Strangely, there are RESI entries for hexane in top_all27_prot_lipid.inp
(although not in all versions I found) but not for octane. There is an
octane entry in
toprna10r_22.inp but the atom type nomenclature is different. Does somebody
have or know of consistent CHARMM topology or parameter files that include
octane? If not, is it feasible for a semi-beginner to write an octane entry
? Am I
correct in assuming that only the topology file would have to be modified,
not the
parameter file.
Thanks in advance for your help.

Michel Seigneuret
Institut Cochin, U567-UMR8104
Département de Biologie Cellulaire
22 rue Méchain, 75014 Paris, France
Tel: 33 (0)1 40 51 64 50
Fax: 33 (0)1 40 51 64 54

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