Hi Jason,
Thanks a lot for your answers. The *'s are actually probably because I put
my input file in bold in Gmail, and Gmail uses *'s to make text bold. Those
aren't there in my raw input files.
The first minimization input file is the stage where I see the problem.
Thanks a lot for your help, Jason, and have a great day,
Kamali
On Tue, Aug 2, 2011 at 7:51 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Where are the *'s coming from? Are they actually in your input file? I
> can't imagine your input file would actually work if the *s were there.
> I'm
> going to comment as though your *s are not there:
>
> Also, which step did the error occur on? I just want to know which input
> files caused errors.
>
> On Tue, Aug 2, 2011 at 7:31 AM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
>
> > Hi Jason,
> >
> > Thanks a lot for your response, and I'm sorry that I forgot to attach the
> > mdin file.
> >
> > Here is the first minimization file:
> >
> > * &cntrl*
> > * nmropt=1,*
> > * imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1,*
> > * cut=9.0, nsnb=10, ntr=1, maxcyc=1000, ncyc=500, ntmin=1,*
> > * &end*
> > *Group input for DNA restraints: 25 kcal/mol.*
> > * 25.0*
> > *RES 1 73*
> > *END*
> > *END*
> > *DISANG=DISANG*
> >
>
> You need to actually have some &wt namelist here that informs sander that
> you want a distance restraint. See section 2.8 in the Amber11 manual for
> instructions on how to do this properly.
>
> *
> > *
> > Here is also the thermalization input file, which is the next step in my
> > equilibration protocol. I'm attaching this here because for this file,
> the
> > flag nmropt=1 was already set, and I'm wondering if adding the DISANG
> > variable will mess anything up in this file:
> >
> > * &cntrl*
> > * imin=0, ntx=1, ntpr=500, ntwr=500,*
> > * nscm=5000,*
> > * ntf=2, ntc=2,*
> > * ntb=1, ntp=0,*
> > * nstlim=50000, t=0.0, dt=0.002,*
> > * cut=9.0,*
> > * tempi=100.0, ntt=1,*
> > * ntr=1, nmropt=1*
> > * &end*
> > *Heating from 100 to 300 K*
> > * &wt type='TEMP0', istep1=0, istep2=5000, value1=100.0,
> value2=300.0,
> > &end*
> > * &wt type='TEMP0', istep1=5001, istep2=50000, value1=300.0,
> value2=300.0,
> > &end*
> > * &wt type='END', &end*
> >
>
> The only NMR options specified here are varying the TEMP0 value; it says
> nothing about actually reading in any kind of distance/angle/dihedral
> restraints.
>
>
> > *Group input for DNA restraints: 25 kcal/mol.*
> > * 25.0*
> > *RES 1 73*
> > *END*
> > *END*
> > *DISANG=DISANG*
> > *
> > *
> > Here again is the DISANG file:
> >
> > *&wt type = 'END', &end
> >
> > &rst
> > iresid=1, iat = 2,37, atnam(1)='N6', atnam(2)='N3',
> > r1=0.0, r2=2.7, r3=3.2, r4=16.0, rk2=50.0, rk3=100.0,
> > &end
> >
>
> Make sure you know what the form of your potential will actually look like
> with the given r#'s and rk#'s. It will be an asymmetric flat-well
> potential
> with no biasing at all between 2.7 and 3.2 angstroms.
>
>
> >
> > &rst
> > iat=0,
> > &end*
> >
>
> There's little point of this last section. You might as well just take it
> out, since you're only creating one distance restraint.
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
>
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Received on Tue Aug 02 2011 - 13:00:03 PDT
