Hi,
does Amber stop after the warning or does it continue after maybe a few
more warnings?
A TI simulation needs all non-softcore atoms to be at the same coordinates
in your two systems. Sometimes that is not exactly so, for example because
xleap translated the systems origins into their (slightly different)
center of masses.
sander will realize this and correct small mistakes up to 0.1 A, but warns
you that it does so. This is normally not a problem, just a reminder that
your system was modified a little bit (which should not change your
results).
Kind Regards,
Thomas
On Fri, July 2, 2010 3:43 am, sunita gupta wrote:
> Hello Everyone
>
> I am calculating the relative binding energy of two ligand using TI. I am
> following the tutorial in which benzene was transformed to phenol.
> While Vwd decoupling (second step) I am getting the following
> error...."WARNING: Local coordinate 1 differs from partner
> coordinate 1 !"
>
> I have searched the Archive but did not get any help. Does anyone know
> what
> does this mean? and how to solve it?
> I am using Amber10 and below are my input files
> *Min1*
> Minimization with restraints
> &cntrl
> imin = 1, maxcyc = 2000, ntb = 1, ntr = 1, cut = 10.0, ntpr=1, ntx=1,
> ntmin=2, icfe=1, klambda=1, clambda=0.95308, ifsc =1, crgmask=
> ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28,N29,H30,H31,H32',
> scmask = ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28,N29,H30,H31,H32',
> /
> Hold the Protein and DRG fixed
> 50.0
> RES 1 1
> END
> END
>
> *Min2*
> Minimization with restraints
> &cntrl
> imin = 1, maxcyc = 2000, ntb = 1, ntr = 1, cut = 10.0, ntpr=1, ntx=1,
> ntmin=2, icfe=1, klambda=1, clambda=0.95308, ifsc =1,
> crgmask=':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28',
> scmask = ':DRG.C19,C20,C21,C22,C23,H24,H25,H26,H27,H28',
> /
> Hold the Protein and DRG fixed
> 50.0
> RES 1 1
> END
> END
>
> *Group File *
> -O -i min1_0.95308 -p new3z.top -o min1_0.95308.out -c new3z.crd -r
> min1_0.95308.crd -x min1_0.95308.mdcrd -ref new3z.crd
> -O -i min2_0.95308 -p new54z.top -o min2_0.95308.out -c new54z.crd -r
> min2_0.95308.crd -x min2_0.95308.mdcrd -ref new54z.crd
>
> Thanks in Advance
> --
> SUNITA GUPTA
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Jul 02 2010 - 02:00:03 PDT
