[gmx-users] [Fwd: gromacs]

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 20 12:09:05 CET 2006

-------- Original Message --------
Subject: 	gromacs
Date: 	Mon, 20 Nov 2006 12:26:02 +0300
From: 	Dmitriy Golubobsky <dmitriy.golubovsky at gmail.com>
To: 	spoel at xray.bmc.uu.se

Dear David,
thank you for your answer.
i've read mailing list, and realise that it is a common question for a
newbee in gromacs. =) that's why i decided not to "spam" in it.
i'll be very approtiate for your help.
i've got monomers of 3 types (A,B,C). they are organic, consists of only
C,H,N,O atoms
really, i use PRODRG to produce topology for them.
1. what i have to add to the *.hdb files?
2. how can i explain gromacs, what bonds to use, to construct monomer?

i really need help. nobody in our department have any idea, how to do this.
i'm a Ph.D. studen of department of pollymers of Moscow State University
my emal there is dng at polly.phys.msu.ru <mailto:dng at polly.phys.msu.ru>

Dmitriy Golubobsky wrote:
  > Dear Guru of Gromacs,
  > i've a new user of this programm, and i've got a problem
  > 1. I've got a polymer consists of N monomers of iso-propyl-acrilamide
  > 2. I use Hyperchem to made a sequence
  > 3 Save it in pdb format in HyperChem
  > 4 Use editconf -f  to create .gro format
  > 5 then i use pdb2gmx with this gro file to make topology file
  > and i've got an error. of course, gromacs don't know about my residue
  > The question is,
  > How to make gromacs know about my residue ( all pollymer chain)
  > or 1 monomer, and to make pollymer chain with it.

make a residue definition in the rtp file belonging to the force field
of your choice. you also need to edit the hdb file.
then run pdb2gm on the pdb file.
  > --
  > Dmitriy Golubovsky

Dmitriy Golubovsky

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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