Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint?

From: case <>
Date: Sat, 30 Nov 2013 11:39:44 -0500

On Sun, Dec 01, 2013, zhongqiao hu wrote:

> As Ross suggested (, pmemd
> should support center of mass restraint. But I failed to use it.

The comments in the nmr_calls.F90 file say this:

The only COM restraints allowed are for distances.

> the file 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 = '')
> Fortran runtime error: Bad data for namelist object igr2

I don't immediately see the problem here, but maybe it is moot, since you
won't have success anyway. Does the same input work with sander?

Note that the values of rk2 and rk3 are probably too large.


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Received on Sat Nov 30 2013 - 09:00:02 PST
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