You make an .itp file, which contains the topology of one DPPC molecule. Then in
your topology file (.top) you include the .itp file:
#include dppc.itp
...
...
Further down in the [molecules] section you put
DPPC 189
Regards
Andreas
serdar durdagi wrote:
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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