AMBER Archive (2004)

Subject: Re: AMBER: restrain one tosion angle

From: Yaroslava Yingling (yaray_at_ncifcrf.gov)
Date: Fri Oct 08 2004 - 14:20:09 CDT

Thanks for answering, Carlos. I am using Amber7.
Amber gives me the following info:
           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
                         ** No weight changes given **

 RESTRAINTS:
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints

And proceeds with MD without restrain.
I have another question.
Why do I need to specify weight changes when I want to restrain angle from
-160 to -120 degrees?

Thanks,
Yara

Quoting Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>:

> we would need to see your output file or a good description
> of the error message. does it even look for restraints? does
> it continue with MD, or end in an error?
>
> here are some suggestions:
> 1) what amber version? amber8 needs the restraints in a separate file,
> see the manual
> 2) &wt section goes right after first &end
>
> carlos
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
>
>
> Yaroslava Yingling wrote:
>
> >Greetings,
> >
> >I would like to restrain one torsion angle in one residue in a molecule. I
> tried
> > the following input
> > ...
> > nmropt=1,
> > &end
> > &rst
> > IRESID=0, IAT=386,387,389,398,
> > nstep1=0, nstep2=2000000, imult=0,
> > ialtd=0,r2=-160.0, r3=-120.0, rk2=80, rk3=80.0,
> > &end
> > &wt
> > type='END'
> >&end
> >
> >However, no restrains have been recognised. I obviously missing something.
> I
> >will appreciate some help...
> >
> >Thanks,Yara
> >
> >
> >
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***************************************************************************
Yaroslava G. Yingling, Ph.D.
Laboratory of Experimental and Computational Biology
Center for Cancer Research
National Cancer Institute
NCI-Frederick, Bldg. 469, Rm. 150C
Frederick, MD 21702-1201
Phone: 301-846-5869
Fax: 301-846-5598

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