AMBER Archive (2007)

Subject: Re: AMBER: Fwd: a request

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Thu Jan 25 2007 - 06:44:58 CST

Hi,

As for the atom numbers, your scheme seems OK. The numbers you get
from the PDB file should be correct. You can also try the 'writepdb'
optioin in the qm/mm namelist, that will give you a pdb file with just
the QM region, so you can check your system.

Note that you can also use 'QMMASK' to set the QM region. That may be
easier than listing atom-by-atom.

Now, there's one thing I would *not* recommend you to do, and it is
running the first minimization (just to remove bad contacts) already
with QM. At leas in my experience, you may run into lots of
convergence problems there. You should first minize the system using
just MM, then try to take it to the desired temperature first, all
using MM. AFTER that, you can change part of the system to QM, and
then relax the system for a while more. This procedure seems to work
best for me. (Ross, comments?)

Gustavo.
P.S. If you are running into problems with putting all files in gmail,
you can try to tar all files together and send just one tar file.

On 1/25/07, santanu roy <66.santanu_at_gmail.com> wrote:
>
> Sir, I could not send prmtop and inpcrd file, gmail problem.
> looking forward for your reply.
>
>
> ---------- Forwarded message ----------
> From: santanu roy <66.santanu_at_gmail.com>
> Date: Jan 25, 2007 12:42 PM
> Subject: Re: a request
> To: Ross Walker <ross_at_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_at_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_at_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_at_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_at_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_at_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_at_gmail.com]
> > > Sent: Friday, January 12, 2007 08:31
> > > To: amber_tutorial_query_at_rosswalker.co.uk;
> ross_at_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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