Arun kumar V wrote:
Try PRODRG server to build the molecule as well as to get topology file.
Though you might have to be careful in using this topology file.
If by "be careful" you mean "don't use this topology," I'll agree :) The Gromos
parameters for lipids (at least Gromos87 and Gromos96 43a1, given by PRODRG)
fall far short of reproducing lipid properties. That, and the charges assigned
by PRODRG for lipids will not resemble any known parameter set, requiring a
complete re-write of this topology. You could use PRODRG to build the molecule,
but there are a number of other programs that can do that as well (see the
Gromacs site for a list).
To the original post: What lipid are you looking to simulate? Many
pre-equilibrated lipid bilayers are available in the public domain, along with
suitable paramters, saving you a lot of work in building these systems. They
can be tricky.
-Justin
Arun
Saumya wrote:
Hi all,
Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describes the procedure using Gromacs?
Hoping for some inputs.
Regards
Saumya
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
