kirtana S wrote:
Dear Users,
In the gromacs manual on means to convert the pdb file to gromacs
topology file I need to use pdb2gmx.
Here I have to specify the force field .How to work with organic
residues which do not exists .
Since I had used general amber force field, and could not find this in
the /share/top/ directory .
Do I need to manually construct the .itp file for each residues. What
will be the easiest way to construct
a solvated box with user defined residues in gromacs.
If the residue of interest will be a component of a polymeric molecule like a
protein, refer to
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field.
If the molecule is a standalone species like a ligand, solvent, etc then all
you have to do is #include an .itp file in the system topology.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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