AMBER Archive (2004)

Subject: RE: AMBER: MD simulation : problem

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Sun Jul 11 2004 - 23:53:51 CDT

Hi Ross,
Actually I am trying to see whether water molecules play a role in binding interaction of the ligand with the receptor in my system. I dont know whether there exists any way by which I can add water molecules selectively at the ligand binding site. So that, I can see whether the water molecules move in to the ligand binding groove and take part in the binding interaction.
 Hence I added a water cap by eyeballing the coordinates of my ligand. ( as mentioned in the Streptavidin-Biotin tutorial).But my problem is I dont know what kind of setup should I use for MD simulations. I am using Redhat Linux on AMD Athlon processor Following is my input file-

 heating up the system equilibration stage 1

&cntrl

irest=0,

 ntx=1, tempi=100.0, ntt=1,

temp0=300.0, tautp=2.0, ntp=0,ig=209858,

nstlim=500,dt=.002,

ntc=2, ntf=2,ntwr=500,

ntpr=20, ntwx=500,

nrespa=2,

&end

What I mean by "I tried to run the simulation with periodic boubdary conditions as above (cutoff 12.0) but the system just doesn't go anywhere." that that sander fails to write any output to the md.out file ( it remaims empty). Even in the energy minization steps I have to use ntb=1.

Interestingly, when I turn on the periodic boundary conditions (ntb=0) then the simulation runs fine. So my problem is how do I add water molecules selectively and the binding site? If there is any way to do this then shall I run the simulations with periodic or non-periodic conditions?

 

Thanks in advance

Regards

Sachin Patil

------------

Dept. of Medicinal & Biological Chemistry

Univ. of Toledo Toledo, Ohio, 43606

Ross Walker wrote:
Dear Sachin,

If you are trying to observe the movement of the water molecules you are unlikely to learn much bu having a water cap of jut 32 water residues. The reason for this is that the outer water molecules of the cap has a restraining force that acts to keep them as part of the water cap and so stop them boiling off into vacuum. With only 32 water molecules in the cap a large proportion are going to be restrained and so the movement of the water molecules is going to be un-representative of a bulk system.

I'm not sure what you mean by the statement "I tried to run the simulation with periodic boubdary conditions (cutoff 12.0) but the system just doesn't go anywhere."

Are you implying it runs very slowly (what computer spec do you have and how big is your system) or that something is wrong with the MD. Ideally if you can afford it you want to run periodic boundary conditions with your entire system solvated in a box of water. Typically you want a buffer size of at least 10A around the entire protein. If you cannot afford such an expensive calculation then try a solvent cap or implicit solvent but be aware of the limitations. Especially with regard to things being restrained in the solvent cap case.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

---------------------------------
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of sachin patil
Sent: 11 July 2004 08:08
To: amber_at_scripps.edu
Subject: RE: AMBER: MD simulation : problem

Hi Ross,
Thank you for you suggestions. It really helps a lot.
Actually, I have solvated my system with a water cap (32 water residues) and I am trying to see the movement of the water molecules.
I tried to run the simulation with periodic boubdary conditions (cutoff 12.0) but the system just doesn't go anywhere. So I switched to nonperiodic conditions as mentioned
in the Streptavidin Biotin tutorial.
But my problem was that I was not sure whether I am correct in using non-periodic
conditions for my system.
So my questions is how do one selectes whether he should use periodic or non-periodic conditions for his system?

Thank you again

Regards
Sachin Patil
-----------------
Dept. of Medicinal & Biological Chemistry
University of Toledo, Toledo
Ohio 43606

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