From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Fri Jan 26 2007 - 12:33:18 CST
Thank you Gumbart,
so now
1) if i am not defining any of my protein atoms as smd-atoms, why should it
be pulled along with my ligand (since the force is being applied to only the
ligand [smd-atoms])? In my case the ligand is bound with 4 H-bonds with the
protein.
2) Also if i restrain my protein, will it not effect the MD of my protein in
some way?
thank you again
narender
1) What direction do you want to pull it in? Presumably away from the
protein along some path; you will have to decide this. You may find however
that you will need to restrain the protein in some way, otherwise you will
likely pull it right along with your ligand!
2) The center of mass does not become the smd atom as the center of mass is
still just a fictitious point. When you define all the atoms as smd atoms,
effectively the center of mass is pulled, but the force is applied to all
the atoms weighted by their masses.
3) Actually, a timestep of 1 fs is best for any MD, but I don't think there
is any unique benefit in the case of SMD (someone correct me if I missed
something). Don't forget though, the SMD velocity is defined in terms of
Angstroms/timestep so if you use 2 fs, then your real velocity will be half
what is in the configuration file.
On Jan 26, 2007, at 11:11 AM, Narender Singh Maan wrote:
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
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
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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