AMBER Archive (2004)

Subject: RE: AMBER: MD simulation : problem :THANK YOU

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Tue Jul 13 2004 - 09:51:28 CDT

Hi Ross,
 Thank you for such a detailed reply. I know, as a
beginner I may have some doubts which sound a bit
crazy.But I really appreciate your help and patience,
 It really helps a lot.

Thank you again,

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

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Hi Sachin,
>
> First of all a couple of things that I don't know if
> are due to a typo in
> your message below. ntb:
>
> ntb = 0 (NO periodic boundaries - don't use this if
> you have solvate with a
> BOX of water)
>
> ntb = 1 Periodic boundaries (PME) constant volume.
> Use when minimising and
> initally heating / equilibrating your system.
>
> ntb = 2 Periodic boundaries (PME) constant pressure.
> Use for a production
> run once you have heated and equilibrated at
> constant volume.
>
> Your message seems to suggest that you don't get any
> output when ntb>0. I.e
> when periodic boundaries are turned on. This is not
> good and suggests that
> you may have a problem with your amber installation
> (although you don't
> specify how long you let the job run for, with
> buffered output it can
> sometimes be a while before anything is written to
> the output file). I would
> make sure you run the test cases and check they
> complete successfully.
>
> Now, on to the simulation. what I would do is as
> follows...
>
> 1) Take your gas phase pdb initial structure and
> manually work out where you
> want the initial water molecules to be. Then
> manually add these, say 3 or 4
> water molecules, to the pdb file with residue name
> WAT.
>
> 2) Visualise this structure and check the water
> molecules are in a
> reasonable position in the binding site.
>
> 3) Minimise this system (ca. 500 steps) in gas phase
> with large cut off and
> ntb = 0. This step may not be necessary depending on
> how well you placed the
> water molecules... Check the structure after
> minimisation to see if it is
> still reasonable... ambpdb -p prmtop <restrt
> >minimised.pdb
>
> 4) Load the minimised pdb into leap, charge
> neutralise and then solvate with
> TIP3P water:
>
> solvate unit TIP3PBOX 10.0
>
> Check how many water molecules this adds and thus
> the total number of atoms
> in your system. Note, if you have more than 20,000
> atoms or so you are
> likely to have a hard time on a single cpu machine.
> I recommend running on a
> cluster of 4 or 8 cpus at least...
>
> 5) Minisize the system in two stages, water first
> with 'weak' restraints on
> protein. Then entire system...
>
> 6) Heat from 0 to 300K with ntb=1 and ntt=3,
> gamma_ln=1.0, over about 20ps
> or so... ntx=1, irest=0
>
> 7) switch to ntb=2 and run production md (ntx=5,
> irest=1 and give it the
> restrt file from 6 as the coords -c restrt) for as
> long as you need with
> tempi=300 and temp0=300, ntt=3 and gamma_ln=1.0.
> Note, depending on the
> timescales of what you hope to see you may need to
> dump to the mdcrd file
> fairly regulary, say every 50fs or so,
> ntpr=50,ntwx=50 (note it will get
> VERY BIG, if it exceeds 2GB you will probably need
> to split your sim into
> several stages).
>
> 8) Take a look at the results...
>
> Note, if your system starts blowing up, which it may
> well do then you will
> need a much more elaborate minisation and
> equilibration scheme...
>
> 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 21:54
> To: amber_at_scripps.edu
> Subject: RE: AMBER: MD simulation : problem
>
>
> 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
>
>
>
=== message truncated ===

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