[gmx-users] tutorial for membrane-bound systems

[Andreas]

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 <anoddlad at yahoo.com>/* 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 <durdagis at yahoo.de>
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>     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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-- 
Dr. Andreas Kukol
Senior Lecturer in Biochemistry
School of Life Sciences
University of Hertfordshire
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