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*
*
*
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*
*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
&rst
iat=0,
&end*
*
*
and finally, here is the error I've been getting (just to put everything in
one email):
* ----- READING GROUP 1; TITLE:
*************************************************************************
rfree: Error decoding variable 1 3 from:
*****************************
this indicates that your input contains
incorrect information
field 1 was supposed to
have a (1=character, 2=integer, 3=decimal) value
*
*
*
Sorry for the long email, and thanks again, Jason,
Kamali
On Mon, Aug 1, 2011 at 11:41 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Please attach all of your input files (your MDIN file as well as your
> DISANG
> file).
>
> rfree is a method that is called when reading group inputs (it's a
> "free-format" parser of sorts). It's gotten to the point where it expects
> a
> string then a decimal value, but based on the information you've given us I
> can't tell why that is. That is, this is failing while reading the MDIN
> file (illegal syntax somewhere), not in reading the DISANG file.
>
> All the best,
> Jason
>
> On Mon, Aug 1, 2011 at 5:57 PM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
>
> > Dear AMBER users,
> >
> > I have a question about using NMR restraints during minimization in
> > AMBER10/11. I want to restrain certain hydrogen bonds during
> minimization,
> > and I'd like to use the nmropt=1 flag. I have a 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
> >
> > &rst
> > iat=0,
> > &end*
> >
> > However, I keep getting the same error message at the end of my first
> stage
> > of minimization. I've tried to change the position of the DISANG variable
> > at
> > the end of my mdin file, and also change the syntax of the DISANG file,
> but
> > neither of these strategies has helped:
> > *
> > ----- READING GROUP 1; TITLE:
> >
> *************************************************************************
> >
> > rfree: Error decoding variable 1 3 from:
> > *****************************
> >
> > this indicates that your input contains
> >
> > incorrect information
> >
> > field 1 was supposed to
> >
> > have a (1=character, 2=integer, 3=decimal) value
> >
> > *I've seen this error pop up multiple times on the AMBER mailing list,
> but
> > I
> > believe that most of these errors were not setting nmropt equal to 1. I
> > know
> > that I've done that in my mdin file, so I'm still unsure as to what the
> > problem is.
> >
> > Any help would be greatly appreciated. Thank you all in advance
> > --
> > Kamali Sripathi
> > Graduate Student, Medicinal Chemistry
> > Walter Laboratory
> > 930 North University
> > Ann Arbor, MI, 48109
> > ksripath.umich.edu
> > _______________________________________________
> > 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
>
>
>
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Received on Tue Aug 02 2011 - 05:00:02 PDT
