Hi, Abir
You can try to use the reaction coordinate DF_COM_DISTANCE in &pmd to add
the restraint. It is working for pmemd. You can check the manual on page
456.
Best
Feng
On Thu, Jul 19, 2018 at 8:49 AM Abir Ganguly <ag1508.connect.rutgers.edu>
wrote:
> Dear AMBER users,
>
> 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]
>
> I tried with both pmemd and sander; with pmemd I am getting the error :
>
> At line 1032 of file nmr_calls.F90 (unit = 33, file = 'rest.RST')
> Fortran runtime error: Bad data for namelist object igr4
> srun: error: cuda001: task 0: Exited with exit code 2
> srun: Terminating job step 7013508.0
>
> with sander I am getting the error :
>
> forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
> 33, file
> /scratch/ag1508/work/vs/dimer/with_mg/c634/trunc3/wt/gdp_ap/str3/12_6_4/pmf/mg/temp2/rest.RST
>
> I guess I am messing up the syntax of the restraint file. I will
> appreciate if anyone can point out any obvious errors with the input.
>
> Thanks,
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>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Thu Jul 19 2018 - 14:30:02 PDT
