Hi Prof. Case, Feng,
Thanks a lot for the replies. I was not aware of the colvar/pmd module in AMBER. It is really useful. My test case is working now.
Best,
On Jul 20, 2018, 10:16 AM -0400, Abir Ganguly <abir.ganguly.rutgers.edu>, wrote:
> Hi Prof. Case, Feng,
>
> Thanks a lot for the replies. I was not aware of the colvar/pmd module in AMBER. It is really useful. My test case is working now.
>
> Best,
> Abir Ganguly, Ph.D.
> Postdoctoral Associate
> Center for Integrative Proteomics Research
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road
> Piscataway, NJ 08854 USA
>
> From: Feng Pan <fpan3.ncsu.edu>
> Sent: Thursday, July 19, 2018 5:13:59 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Distance restraint for PMEMD
>
> 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 Fri Jul 20 2018 - 07:30:03 PDT
