On 9/12/12 1:34 PM, vidhya sankar wrote:
Dear justin ,
Thank you fro your Reply
I am doing MD for Cyclic poly Peptide With ARG as
N-termina and PRO as C-terminal . I have run pdb2gmx it is oak. . I have
solvated and added ions successfully
But when i Run the Energy Minimization The Bond between N atom of ARG and C
atom of PRO is broken .
What Should i Do To keep this Bond Through entire EM and MD ? Can i Use
Constraints option in topology file
if i need to use Constraints option What is the Syntax ? Also The Bond is
not constructed between N atom and C atom of terminal ARG and PRO residues in
Topology
Then you already have your answer. Bonds do not break or form during MD.
pdb2gmx does not produce cyclic polypeptide topologies unless you have made
appropriate modifications. As you are observing, there is no such bond and you
need to add it (and any other resulting bonded parameters like angles,
dihedrals, and impropers) yourself.
-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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
