This might sound trivial ... and I dont know if that's the source of any
errors ... but just glancing at the input, i realized that it misses a
comma after ntwr=2000 (last line).....
I have no idea if that creates any problems .... but all my scripts have
commas before the end character "/" ....
From my experience with AMBER, crashes that do not output any errors
(as Urszula reported) are the result of input namelist errors ....
As for LES, most crashes that I had to deal with were the result of the
instrinsic limits for addles or sander.LES .. but they do report clear
error messages pointing the user to the increase of certain parameters
before re-compilation ....
vlad
Carlos Simmerling wrote:
> it looks ok to me, perhaps you can send prmtop and inpcrd privately
> (not to the whole list)
> and I can try them.
>
> On 6/4/07, *Urszula Uciechowska* <
> urszula.uciechowska.pharmazie.uni-halle.de
> <mailto:urszula.uciechowska.pharmazie.uni-halle.de>> wrote:
>
>
> Dear Amber users,
>
> I would like to run LES simulations on an loop. I have the non-les
> system equilibrated (water
> +ions) and I created the LES topology (starting from the
> equilibrated non-LES system) file by
> making 5 copies of my region. After running sander.LES I am
> getting only the empty out file
> and nothing more I checked my prmtop file and it seems to be ok
> and also copies that I made.
> I copied my input file below that I would like to use to LES,
> maybe there are some mistakes.
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 9, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 298.15, temp0 = 298.15,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.002,
> ntpr = 200, ntwx = 200, ntwr = 2000
> /
>
> sander.LES -i LES_p.in -o LES_p.out -p LES_p.prmtop -c LES.x -r
> LES_p.restrt -x LES_p.mdcrd
>
> Thank you for any help,
>
> Urszula
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
>
> ----- Original Message -----
> From: David Cerutti <dcerutti.mccammon.ucsd.edu
> <mailto:dcerutti.mccammon.ucsd.edu>>
> Date: Monday, May 21, 2007 3:15 pm
> Subject: Re: AMBER: Pi-pi interactions
> To: amber.scripps.edu <mailto:amber.scripps.edu>
>
> > No, there are no pi-pi interactions in any of the AMBER
> > forcefields. This
> > is a quantum effect, and is not treated in any classical
> > forcefield.
> > Emulation of this effect can come about only via favorable van-der
> > Waals
> > interactions, and hopefully the physics is not upset by the qq/r
> > point charge interactions.
> >
> > Dave
> >
> >
> > On Mon, 21 May 2007, Roberto Veiga wrote:
> >
> > > Dear all:
> > >
> > > are the Amber force fields suitable to this kind of interaction
> > (pi-pi)?
> > >
> > > []s,
> > >
> > > Roberto
> > > ------------------------------------------------------------------
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>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail:
> carlos.simmerling.gmail.com <mailto:carlos.simmerling.gmail.com>
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
--
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Dr. Vlad Cojocaru
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Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
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Received on Wed Jun 06 2007 - 06:07:30 PDT
