Ravi Kumar Venkatraman wrote:
Dear all,
I have generated .gro and .top file for Chloranil from
prodrg and tried solvate it using pre-equilibrated cyclohexane. When i
tried to generate the box containing solute it is not modifying the .top
file and it shows zero solvent.
Please help me how to solvate organic molecules that are obtainde from
prodrg.
genbox only adds SOL entries, nothing else. Modify the topology by hand.
Hopefully you have already done a proper parameterization, as the results from
PRODRG are likely to be quite inaccurate:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-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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