The error message says it all. PMEMD does not support all of the same
restraints as SANDER.
I believe the center of mass restraints are the ones not implemented.
Regards,
Brian
P.S. To developers: Is there an implementation/performance reason for this
difference in features or is it just because coding up all of those
difference restraints involves a lot of time and effort for something so
specialized and rarely used?
On Tue, Oct 8, 2013 at 1:21 PM, Sourav Purohit <sour000.gmail.com> wrote:
> Hi,
>
> I am using the following restraint file to restrain a dihedral and two
> distances.
>
>
> &rst
> iat=393,399,239,234,
> r1=-30.0, r2=150.0, r3=150.0, r4=320.0,
> rk2=300.0, rk3=300.0,
> &end
>
> &rst
> iat= -1, -1,
> igr1= 11,12,14,15,16,17,18,20,21,24,25,26,28,31,
>
> 234,235,237,239,240,243,244,245,246,248,251,
> igr2=
>
> 360,361,363,365,366,369,370,371,372,374,377,389,390,392,393,394,395,396,398,399,402,403,404,406,409,
> r1=-5.0, r2=2.5, r3=2.5, r4=10.0,
> rk2=400.0, rk3=400.0,
> &end
>
> &rst
> iat= -1, -1,
> igr1=
>
> 106,108,109,111,113,114,117,118,119,120,122,125,137,138,140,141,142,143,144,146,147,150,151,152,154,157,
> igr2=
>
> 263,264,266,267,268,269,270,272,273,276,277,278,280,283,486,487,489,491,492,495,496,497,498,500,503,
> r1=8.8 ,r2=22.0 ,r3=22.0 ,r4=35.0,
> rk2=300.0 rk3=300.0,
> &end
>
> Here igr1 and igr2 contain atom nos. , the distance between whoes COM is to
> be restrained
>
> When i try to apply these restraints in PMEMD I get the following error.
>
> *"PMEMD only supports atom groups in distance restraints!*
> *Please use SANDER instead!"*
>
>
> *Kindly tell the reason for this. Is the restraint definition wrong?*
> *
> *
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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Received on Tue Oct 08 2013 - 11:00:03 PDT
