On 6/29/12 2:21 PM, Parvez khan wrote:
Hi, I am trying to do polymer simulation with gromacs. I am new to
gromacs and trying to construct topology for a system of polymer
chains. My problem is that i am facing difficulties to creat pdb file
for polymer chain containing 1000 monomers. I have used PRODRG server
but it gives me a pdb and topology file up to maximum 41 monomers
chain. I am not understanding what wrong with PRODRG server. Is there
Nothing is wrong. It's just that PRODRG limits how many atoms are allowed in
the input structure.
any server or tool for generating db file.
There are lots of ways to generate a coordinate file. Here are some
suggestions:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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