[gmx-users] modeling of polymer(Ni-iso propyl acrilamide)

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 19 14:12:48 CET 2006

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
> ------------------------------------------------------------------------
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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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