sander expects the weight change section then restraints, so if they are
in the
wrong order it might not read them. try putting the &wt section before
the &rst
and see if it works better. otherwise I'm not sure what's going on, we
can check other
things if it still doesn't work.
===================================================================
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.stonybrook.edu
===================================================================
Yaroslava Yingling wrote:
>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.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.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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Received on Fri Oct 08 2004 - 22:53:00 PDT
