On Wed, May 4, 2011 at 3:42 PM, souvik sur <souviksur.hotmail.com> wrote:
>
> Dear Sir,
> thank you sir for your kind response, i have downloaded the AmberTools 1.5
> from your given site and also untarred it and run it as written in the
> direction web page but still antechamber is not running properly as i took
> the example of sustiva.pdb file for practice, can you please send me the
> command lines by which i can run the tools properly,
No. The tools are designed to be flexible, so there is no one-size-fits-all
set of commands to run any of the programs. You will need to invest time in
looking at the manual and learning how the programs work in order to use
them successfully.
List responders can help debug SPECIFIC issues you may have (give details,
like error messages, exact commands, etc.), but we can't do your project for
you (even if we had time, your email doesn't even say *exactly* what you're
trying, anyway).
The best way to ensure that you get responses from the list is to show that
you have an idea of what you want to do, you've found out what utilities to
use, attempted to use them, and at least tried to debug it yourself.
Other emails are unlikely to generate many responses, and none more helpful
than this one here.
All the best,
Jason
and also tell me if there any need of any compiler for it as i early
> installed openmpi-1.5 file for installing Amber9 in my system.please reply
> as early as possible.
> regards,
> Souvik Sur
> Ph. D. Student
> Department Of Chemistry
> University Of Delhi
> India
>
>
>
>
> > From: psn.berkeley.edu
> > To: amber.ambermd.org
> > Date: Mon, 2 May 2011 22:38:02 -0700
> > Subject: Re: [AMBER] Hardwares requirement
> >
> > Hi Souvik,
> >
> > Not sure what you're looking at, but here's the link:
> http://ambermd.org/AmberTools-get.html
> >
> > Just fill out the form and you're set.
> >
> > Best,
> >
> > Paul
> >
> >
> > On May 2, 2011, at 10:31 PM, souvik sur wrote:
> >
> > >
> > > dear sir,
> > > i see it in the given weblink but can you please send me the link
> > > fom where i can freely download the "Amber tools 1.5".actually it is
> > > not free accessible.
> > > regards,
> > > Souvik Sur
> > > Ph. D. Student
> > > Department Of Chemistry
> > > University Of Delhi
> > > India
> > >
> > >
> > >
> > >
> > >> Date: Mon, 2 May 2011 13:11:29 +0200
> > >> From: jason.swails.gmail.com
> > >> To: amber.ambermd.org
> > >> Subject: Re: [AMBER] Hardwares requirement
> > >>
> > >> There is ample information and benchmarks on the amber website (
> > >> http://ambermd.org) and in the manual.
> > >>
> > >> You should be able to figure it out from there.
> > >>
> > >> HTH,
> > >> Jason
> > >>
> > >> On Mon, May 2, 2011 at 9:38 AM, souvik sur <souviksur.hotmail.com>
> > >> wrote:
> > >>
> > >>>
> > >>> Hello sir,
> > >>> I have amber 9 and working on molecular dynamics, i want to run
> > >>> simulation
> > >>> job for my compounds upto 50ns, can you please suggest me the
> > >>> required
> > >>> configuration of my computer, i use to run simulation job of my
> > >>> compound
> > >>> which has around 40,000 atoms in its structure,please suggest me.I
> > >>> am
> > >>> waiting for your reply.
> > >>> regards,
> > >>> Souvik Sur
> > >>> Ph. D. Student
> > >>> Department Of Chemistry
> > >>> University Of Delhi
> > >>> India
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> Jason M. Swails
> > >> Quantum Theory Project,
> > >> University of Florida
> > >> Ph.D. Candidate
> > >> 352-392-4032
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 04 2011 - 08:00:03 PDT
