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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Received on Fri Jul 02 2010 - 01:00:03 PDT
