abdul wadood wrote:
Dear GMX user
I am working on enzyme ligand complex and want to calculate pmf of the
complex.
I have successfully energy minimized and equilibrated the system.
But when I pull the ligand from the complex using the md_pull.mdp file
then instead of ligand the protein is come out of the system.
Sounds like a normal consequence of periodic boundary conditions. See FAQ #11:
http://www.gromacs.org/Documentation/FAQs
-Justin
I have tried my best to solve the problem but not succeed.
In the md_pull.mdp file I have given 1 for ligand and 0 for protein.
If you kindly help me in this respect I will be very thankful to you.
And your help will be highly appreciated.
regards
Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochem...@hotmail.com
--
========================================
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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