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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Received on Tue Aug 02 2011 - 05:00:04 PDT
