On Nov 30, 2013, at 11:01 AM, zhongqiao hu <zhongqiao.hu.gmail.com> wrote:
> 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.
Pmemd only supports COM for distance restraints.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Nov 30 2013 - 09:00:03 PST
