Re: [AMBER] Distance restraint for PMEMD

From: David A Case <>
Date: Thu, 19 Jul 2018 15:38:47 -0400

On Thu, Jul 19, 2018, Abir Ganguly wrote:
> I am trying to apply a harmonic restraint to a d1-d2 coordinate, where
> d1 and d2 are distances between the COMs of groups of atoms. I found an
> earlier thread on this topic and tried the following in the restraint
> file-
> &rst  iat=-1,-1,-1,-1, igr1=3595, 3596, igr2=3028,
>  igr3=3028, igr4=3032,  rstwt=1,-1,         
>  r1=-999, r2=3.6, r3=3.6, r4=999, rk1=10, rk2=10, /
> In this case my coordinate is :  distance[COM(3595,3596) -- 3028] -
> distance[3028 -- 3032]

Note that rstwt is only available in sander, and you won't be able to
directly use this functionality in pmemd. Maybe someone on the list
knows how/if one can use a distance difference coordinate in pmemd.

> with sander I am getting the error :
> forrtl: severe (19): invalid reference to variable in NAMELIST input,

Unfortunately, some compilers don't give very good error messages when
you have a syntax problem with namelists. You may have to simplify the
namelist down to what works, then slowly add back in variables until you
can see which one the program is objecting to.


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Received on Thu Jul 19 2018 - 13:00:02 PDT
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