AMBER: Fwd: a request

From: santanu roy <66.santanu.gmail.com>
Date: Thu, 25 Jan 2007 14:25:32 +0530

Sir, I could not send prmtop and inpcrd file, gmail problem.
looking forward for your reply.


---------- Forwarded message ----------
From: santanu roy <66.santanu.gmail.com>
Date: Jan 25, 2007 12:42 PM
Subject: Re: a request
To: Ross Walker <ross.rosswalker.co.uk>



 Dear Sir,
                 Let me tell you what I am actually doing. I am using AMBER
qmmm method for simulating Thermolysin. Some part of the Active site
has been kept into the QM region and other part obviously moves into the
MM region. I , atfirst, using Xleap solvated the system of interest i.e.
thermolysin using solvatebox command. Then I made thermolysin.prmtop
and thermolysin.inpcrd file. Then using ambpdb command I made
solvated_thermolysin.pdb , i.e. using parameter and coordinate file and
ambpdb command I have got a new pdb file of solvated thermolysin.

Now, I have to minimise the solvated thermolysin, so atfirst my job would
be to minimise the water solvant keeping thermolysin fixed. There I found
the problem. in iqmatoms=......, I took the atom no. from the newly
formed solvated_thermolysin.pdb. I have a doubt over here, as when we
run the command for minimisation only prmtop and inpcrd file information
are given, so if we use atom no. in qmmm key , taken from
Solvated_thermolysin.pdb which is made from prmtop and inpcrd file,
will that be correct? Actually there is no other way to assign atom no. in
qmmm key I have found. I think I am right in this case.

I am attaching the input and output file, and also prmtop & inpcrd file,
solvated_thermolysin.pdb file.

I am using SGI ALTIX, MPIRUN, sometimes using 8 parallel processor
and sometimes 4 parallel processor.





On 1/24/07, Ross Walker <ross.rosswalker.co.uk > wrote:
>
> Hi Santanu,
>
> The input format for QMMM with link atoms is identical to QMMM without
> link atoms. Sander takes care of all the link atom treatment for you
> automatically. The best is if you can send me the calculation you are
> running so I can take a look at it. Please send me the mdin, prmtop and
> inpcrd files as well as the output file where you are having problems.
>
> It would also be useful to know what system (OS, processor etc) you are
> running this on, what compilers you used. Is this serial or parallel? And
> which bugfixes have been applied to the Amber installation?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* santanu roy [mailto:66.santanu.gmail.com]
> *Sent:* Wednesday, January 24, 2007 01:11
> *To:* Ross Walker
> *Subject:* Re: a request
>
>
>
> Dear Sir,
> Thank yoy very much for your reply. I have got my answer.
> But I am facing problem while silmulating qmmm system.
>
> Can you please send me the input formate for qmmm with link atom method.
> Neither in the tutorial , nor in the manual the qmmm formate including link
> atom is given. I myself tried out, but getting some error like
> 'aborting' .
>
> I will be highly obliged if you kindly respond.
> Thanking you,
> Santanu
>
>
>
> On 1/17/07, Ross Walker <ross.rosswalker.co.uk > wrote:
> >
> > Dear Santanu,
> >
> > I'm not entirely sure I understand your question correctly. However, I
> > assume you are refering to the first amber tutorial on modelling DNA. Here
> > we start doing gas phase simulations where we run two simulations, one
> > without a cutoff and one with. The key point here is that the cutoff
> > simulation gives a stable system but the no-cutoff simulation does not. Thus
> > one could make the "wrong" conclusion that the cutoff sim is giving the
> > correct result. However, these simulations are in a vacuum at 300K. If I
> > really took a 10mer of DNA and heated it up to 300K in a vacuum it would not
> > be stable - the two chains would alsmost certainly come apart and the
> > molecule would decompose. Thus the no-cutoff simulation is probably correct.
> >
> >
> > The important point is that using a cutoff is 'never' a good idea. You
> > can get away with something liek 16 angstroms or more in an implicit solvent
> > GB simulation as there is a dielectric screening factor that reduces things
> > by a factor of 80. However, realisticlly here one should not use a cutoff if
> > one can afford it computationally. Electrostatic interactions are so long
> > ranged that you have to go to 30 or 40 angstroms before you get down to
> > noise.
> >
> > However, with PME doing periodic boundaries the situation is slightly
> > different. You should probably read up on thePME method from the papers
> > cited in the Amber manual and make sure you understand the mathematics.
> > Essentially what you do is take what is a divergent (infinite) sum of pair
> > wise interactions in real space and cast it into a convergent sum in
> > reciprocal space. You then use an FFT to calculate the reciprocal space
> > contribution. You still have a cutoff of say 8 angstroms or so to account
> > for VDW interactions and also for load balancing issues. This way 8
> > angstroms worth of electrostatics is done in the direct space sum within the
> > cutoff while the remainder is done in reciprocal space and adjusted by an
> > erfc function (error function) to go to zero at the cutoff. In this way PME
> > gives you effectively infinite electrostatics without requiring you to
> > calculate infinite pairwise interactions. Hence why you can essentially use
> > a cutoff with periodic boundaries without problems - as LONG AS YOU ARE
> > USING PME.
> >
> > I hope this helps explain things. Note if you further questions it is
> > probably best to post them to the Amber mail reflector - see
> > http://amber.scripps.edu for details on how to subscribe.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> > ------------------------------
> > *From:* santanu roy [mailto:66.santanu.gmail.com]
> > *Sent:* Friday, January 12, 2007 08:31
> > *To:* amber_tutorial_query.rosswalker.co.uk; ross.rosswalker.co.uk
> > *Subject:* a request
> >
> >
> > Dear Sir,
> > I have gone through almost all of the amber tutorial,
> > and tested it.
> >
> > I have some basic questions as the following
> > 1) why we generally take cutoff as 8 to 10 angstrom? in this case we
> > get actually correct result, why? in case of no cutoff we get
> > worst result. why?
> > is it like VDW interaction, electrostatic interaction get very less
> > value, so we should ignore those interaction after that cut off?
> > and in case of no cut off we consider those interactions, is it the
> > reason for unstable result?
> >
> > 2) does cut off affect on periodic boundary condition?
> >
> > I am looking forward for your answer.
> > Regards
> > Santanu Roy
> >
> >
> >
>



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Received on Sun Jan 28 2007 - 06:07:15 PST
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