From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Jan 26 2007 - 11:11:39 CST
Dear Users,
I have some questions about setting up my system (a protein-ligand system
with constant velocity SMD)…In this i am trying to pull the ligand out of
the protein. So,
1) as it says in namd/smd tutorial it keep one atom fixed (beta 1) and
smd-atom moving (occupancy 1)…but in my situation i just want to pull the
ligand out of the protein's binding site and do not want to keep anything
fixed (in protein). So in this situation I have all my beta column set to
zero. So the question is how do I find out the vector direction? (since it
requires to find the vector direction that links fixed and smd atom, and I
don't have the fixed atom!)
2) I can define a fixed Center of mass of my ligand and make it as
smd-atom and pull it out from that point but how can I define all the atoms
(as smd-atoms) of my ligand and pull them out together?..
3) Many of the related papers that I see for SMD shows the timestep of
1fs!!..why is it so??..normally in MD we keep it 2fs…..is it that SMD is
more stable with 1fs timestep??..
This here is my coordinate *xx.pdb* file (segname PRO1 is my protein part
and segname INH1 is my ligand)
ATOM 3670 HG23 THR 234 -2.295 20.477 -15.764
0.00
0.00 PRO1
ATOM 3671 C THR 234 -5.395 20.707 -12.464
0.00 0.00 PRO1
ATOM 3672 OT1 THR 234 -6.336 20.719 -13.291
0.00
0.00 PRO1
ATOM 3673 OT2 THR 234 -5.441 21.306 -11.370
0.00
0.00 PRO1
ATOM 3674 C29 RPR 1 -1.666 -5.800 10.832
0.00 0.00 INH1
ATOM 3675 N30 RPR 1 -2.030 -6.192 9.650
0.00 0.00 INH1
ATOM 3676 H30 RPR 1 -2.660 -6.969 9.662
0.00 0.00 INH1
This here is my smdfile *xx.ref* file
ATOM 3670 HG23 THR 234 -2.295 20.477 -15.764
1.00
0.00 PRO1
ATOM 3671 C THR 234 -5.395 20.707 -12.464
1.00 0.00 PRO1
ATOM 3672 OT1 THR 234 -6.336 20.719 -13.291
1.00
0.00 PRO1
ATOM 3673 OT2 THR 234 -5.441 21.306 -11.370
1.00
0.00 PRO1
ATOM 3674 C29 RPR 1 -1.666 -5.800 10.832
1.00 0.00 INH1
ATOM 3675 N30 RPR 1 -2.030 -6.192 9.650
1.00 0.00 INH1
ATOM 3676 H30 RPR 1 -2.660 -6.969 9.662
1.00 0.00 INH1
And this here is a part of my xx.conf file
___________________________________________________________________
fixedAtoms on
fixedAtomsFile xx.ref
fixedAtomsCol B (???)
SMD on
SMDfile xx.ref
SMDk 5;# 347.395 pNA
SMDvel 0.00001 ; # 10A/ns since ts is 1fs
SMDDir -0.3534 -0.4135 0.8391 ; # (??just a test)
SMDOutputFreq 100
__________________________________________________________________
Any suggestions would be of great help
Thank you
singh
P.S. I searched the list for these questions but please pardon me if i have
missed the already answered related questions.
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