[gmx-users] help - pr
hayagrivar at hotmail.com
Fri May 19 11:05:39 CEST 2006
1.i'm trying to dock my protein with the ligand.for the ligands i want to do
energy minimization.shall i do em.mdp step alone to get the energy minimized
ligand structure for my docking studies.can i make use of that structure
which got out of using gromacs software with the energy minimization step
alone..........or else i've to continue full dynamics step........
2.one more doubt is how to fix up the time for equilibration step.i set
500ps for my protein to do pr.........but i do not know whether it is
correct or not.the thing is i want to know how much time the PR step sh'd be
carried out...if it depends upon our protein length means also - how?
thank u in advance.
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