Dear amber users
I am trying to perform thermodynamic integration using soft core potentials
(like tutorial A9).
I want to investigate free energy changes in mutation of the dna (GC base
pair ---> AT base pair).
I do first step (removing charge of G9 and C18).
But after mpirun -np 4 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile
min.group,I am faced with
the error in reading namelist cntrl.
my input files are as follows:
min_vo.in
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000, ncyc = 1000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1
ifsc = 0,
crgmask ="
scmask ="
/
min_v1.in
&cntrl
imin = 1, ntx = 1,
maxcyc = 2000, ncyc = 1000,
ntpr = 100,
ntf = 2, ntc = 2,
ntb = 1, cut = 10.0,
icfe = 1, clambda = 0.1
ifsc = 0,
crgmask = :DG9.O6,H1,N2,H21,H22
crgmask = :DC18. N4,H41,H42,H5
scmask ="
/
Any help will highly appreciated.
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Received on Mon Feb 06 2012 - 08:00:03 PST
