On 7/1/12 12:02 AM, Raj wrote:
Dear Justin,
I've tried what you have suggested. I have used the pull code and gave 4
amino acid residues as a reference group. The location of the groups are one
below the ligand (in the protein core) and 3 were on the above ( towards the
active site gorge). When i used the code
This sounds like a poor approach. If you have some residues that are internal
and some that are external, mdrun won't do any productive pulling. Define one
group in a concerted area as a reference group and pull with respect to it to
move the ligand.
-Justin
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DRG
pull_group1 = reference groups
pull_rate1 = 0.003 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
the ligand migrated more and more towards the protein , not coming out of
the protein through the channel i defined by referring the amino acid groups
when I tried with pull_geometry = position, the pull_vec i gave as 0 0 1 and
pull_initial = 0.1 but the grompp ends up with an error saying pull_vec can
not be zero.
when i was trying to use pull_geometry = direction the system blowed up. but
the pull_geometry = distance worked well.
please give me a suggestion to resolve the issue
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--
========================================
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
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