As Ross suggested (
http://archive.ambermd.org/201301/0155.html), pmemd
should support center of mass restraint. But I failed to use it.
I want to put an angle restraint.
the mdin file is as follows
Stage equil
&cntrl
imin = 0, irest = 1, ntx = 5,
nstlim = 5000, dt = 0.002,
ntpr = 5000, ntwr = 5000, ntwx= 5000,
ntc = 2, ntf = 2,
cut = 10.0, ntb = 1,
temp0 = 310.0, ntt = 3, gamma_ln = 2.0,
ntp = 0, pres0 = 1.0, taup = 2.0,
nmropt = 1,
&end
&wt
type='DUMPFREQ', istep1=50,
&end
&wt
type='END',
&end
DISANG=disang_95.in
DUMPAVE=angle_95.dat
the file disang_95.in is
Harmonic restraints for angle
&rst
iat=-1,-1,-1,
r1=-180.0, r2=95.0, r3=95.0, r4=180.0,
rk2=40000, rk3=40000,
igr1=1120,1134,1148,1164,1179,1203,1230,1236,
igr2=4850,4865,4885,4907,4919,4930,4949,4960,
igr3=7499,7506,7516,7540,7555,7561,7584,7590,
&end
Whenever I used pmemd, it always immediately showed error:
At line 1008 of file nmr_calls.F90 (unit = 33, file = 'disang_95.in')
Fortran runtime error: Bad data for namelist object igr2
If I remove the line "igr2=...." and change the line "iat=-1,-1,-1" to
"iat=-1,4850,-1", then it showed error:
At line 1008 of file nmr_calls.F90 (unit = 33, file = 'disang_95.in')
Fortran runtime error: Bad data for namelist object igr1
pmemd only works after I totally removed center of mass restraint.
But sander did run for center of mass restraint.
I know pmemd.cuda does not support center of mass restraint. But does pmemd
support it or not? I am using amber12.
Best regards,
Zhongqiao Hu
Bioinformatics Institute
A*STAR, Singapore
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Received on Sat Nov 30 2013 - 08:30:03 PST
