I recommend the GROMACS manual. Particularly chapter 5.
Oh, and the wiki - http://wiki.gromacs.org/index.php/Category:Tutorials
----- Original Message ----
From: serdar durdagi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Thursday, March 20, 2008 8:52:15 AM
Subject: Re: [gmx-users] tutorial for membrane-bound systems
Dear Alan,
You are right a DPPC unit has less than 300 atoms, but I have 189 units. How
can I apply PRODRG for 189 different coordinate files to convert to necessary
GROMACS coordinate file? It must be very tedious.
I am using ligand-enzyme tutorial for Gromacs. But for membrane-bound case I
guess this tutorial is not enough to work.
Best Wishes,
Serdar
Alan Dodd <[EMAIL PROTECTED]> schrieb:
Firstly, a molecule of DPPC has less than 300 atoms.
Secondly, I'd suggest you look for stuff by Tieleman, White, or Sansom.
Googling/literature searching any of these names with "membrane" should give
you some rough pointers on how it's been done in the past.
There is no official membrane tutorial, however. There is a ligand/receptor
one out there somewhere I think?
----- Original Message ----
From: serdar durdagi <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
Sent: Thursday, March 20, 2008 2:00:49 AM
Subject: [gmx-users] tutorial for membrane-bound systems
Dear all,
I would like to make MD simulations of a drug at the binding site of the
receptor sorrounded by DPPC.
pdb coordinate file of all DPPC units (189 units, 1 unit has 130 atoms) are
described seperately. I was using Dundee PRODRG server for generating .itp and
drgpoh2.pdb files for the drug. Since this program is limited to convert files
up to 300 atoms, I couldn't use it for the DPPC units for constructing a full
drgpoh2.pdb file for the DPPC.
Is there any tutorial of GROMACS for this kinds of systems?
Kind Regards,
Serdar Durdagi
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