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.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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