Dear Amber users,
we try to run a potential-of-mean-force calculation of the
modification of a porphyrin molecule inside a proten. We want to
exclude the energy contribution from the porphyrin using INTPRT=0 and
defining the whole porphyrin as the perturbed group (but without any
perturbation in the charges or atom types). However, such a
calculation gives the same result as one with INTPRT=5.
Is it not possible to exclude the intra-perturbed group energies this
way or have done any silly mistake? We use GIBBS Version 5.
This is the gibbs input file:
Title
&cntrl
isldyn=-2,nstmeq=20,nstmul=20,amxmov=0.2,
amxrst=0.5,almdl0=0.0010,dlmax=0.010,
idifrg=1,isande=1,almda=1.0,
idsx0=-1,ielper=0,ncorc=1,intprt=0,
irest=0,ntx=5,init=4,
nrun=100,nstlim=10000,dt=0.0005,
temp0=300.0,ntt=1,tautp=0.2,
ntc=1,ntf=1,ishkfl=1,
nsnb=50,cut=15.0,cut2nd=20.0,
idiel=1,dielc=1.0,
scnb=2.0,scee=1.2,
ntpr=1000,ntwx=-1,ntwv=-1,ntwe=-1,ndmpmc=1,
ntb=0,ntp=0,taup=0.2,
ibelly=1,ivcap=1,natcap=4923,itimth=1,iperat=4,
intr=1
&end
GRP1
ATOM 49 1034
ATOM 1271 1535
ATOM 5950 9999
END
END
RES -1 308
END
END
4866 4864 4863 4845 0 1 2 1.00000 0.00000
0.00000 999.00000 0.00000 45.00000 0 0
Best regards,
Ulf
--------------------------------------------------------------------
Doc. Ulf Ryde Ulf.Ryde_at_teokem.lu.se
Associate professor
http://signe.teokem.lu.se/~ulf
Department of Theoretical Chemistry Director (studierektor) of
University of Lund postgraduate studies at KC-MNF
Chemical centre, P. O. Box 124 Phone: +46-46-2224502
S-221 00, Lund, SWEDEN Fax: +46-46-2224543
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Received on Mon Jul 23 2001 - 04:18:57 PDT
