cheers! you are a star! :)
On 19 August 2010 20:29, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> The RRES, LRES, RES cards have to come after the &cntrl namelist, not
> inside
> it. They also each need a title, as explained in a recent post. Change
> your mdin file as such:
>
> mdin file
> &cntrl
> ... list variables here ...
> /
> Receptor residues
> RRES # #
> END
> Ligand residues
> LRES # #
> END
> END
>
> Or something to that effect. You can also use mm_pbsa.pl to automatically
> create the input files.
>
> Good luck!
> Jason
>
> On Thu, Aug 19, 2010 at 3:05 PM, g t <sketchfoot.gmail.com> wrote:
>
> > Hi, please excuse me as I do not have a lot of experience with AMBER. I
> > have
> > been finding the correct syntax to use for per residue decomposition. I
> am
> > using amber 10 with the mpi version of sander. I cannot find any example
> of
> > using RRES cards with sander in the manual.
> >
> > my input file for the production run looks like this:
> >
> > NPT
> > production
> > &cntrl
> >
> > imin = 0, ntx = 5, irest =
> > 1,
> > ntpr = 10, ntwr = 1000, ntwx =
> > 0,
> > ntf = 2, ntc =
> > 2,
> > ntb = 2, cut =
> > 9.0,
> > nstlim = 1000, dt =
> > 0.002,
> > temp0 = 300.0, ntt = 3, gamma_ln =
> > 2,
> > ntp = 1, pres0 = 1.0, taup =
> > 2.0,
> > icfe=1, clambda =
> > 0.1,
> > idecomp =
> > 2,
> > RRES 1
> > 10
> > RES 1 10
> >
> >
> > ifsc=0,
> >
> >
> > crgmask='',
> >
> > &end
> >
> > I have tried a variety of other variations, but always get the message "
> > error in reading namelist cntrl". If anyone could help me with my syntax,
> I
> > would be obliged.
> >
> > best regards,
> > GT
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 19 2010 - 13:00:03 PDT
