On 6/29/12 9:38 AM, Raj wrote:
Thanks for your reply Justin.
From your umbrella tutorial I thought the reference group should be the
protein. Now from your reply i think I can specify any amino acid residue in
the protein and I can drive the ligand towards the residue.
where I need to specify the group
If i'm using the pull code
; Pull code
pull = umbrella
pull_geometry = distance ; simple distance increase
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DRG
pull_group1 = ??
These settings are backwards. I'm assuming you're trying to pull the group
"DRG" towards/away from your protein. Therefore, "DRG" is pull_group1 and
whatever your protein reference is pull_group0.
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
how can i specify the residue if i want to pull towards the direction of 3
amino acids, and I've included in the index file
Specify the group name of whatever these residues are as pull_group0.
-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
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