Go through Dan Sindhikara's Tutorila on RISM and 3DRISM, it might solve
your problem
http://www.dansindhikara.com/Tutorials/Entries/2012/1/1_Using_3D-RISM_and_PLACEVENT.html
*Dr. Atul Kumar Jaiswal*
Research Associate
DAILAB
Department of biochemical engineering and biotechnology
Indian Institute of Technology, Delhi
India
On Fri, Aug 7, 2020 at 7:09 PM angad sharma <angadsharma54.gmail.com> wrote:
> I am trying to run the 3D-RISM calculations using rism3d.snglpnt to
> calculate free energy, i got trajectory file of 1000ns from that i had to
> a take 10 frames between 50-100ns. The protein has +26 unit of charge.
> >parm AB.prmtop
> >trajin prod.nc <http://md100ns.nc/> 5001 10000 500
> >strip:WAT
> >strip:Na+
> >strip>Cl-
> >trajout newtraj.nc <http://dnanew.nc/>
> >trajoout 10snapshot.pdb
> >parmwrite out 10snapshot.prmtop
>
> And the command for 3d rism is :
> rism3d.snglpnt --pdb 10snapshot.pdb --prmtop 10snapshot.prmtop --closure
> KH --buffer 45.0 --xvv ../1drism/SPC_NaCl.xvv
>
> it is giving some error i m trying to figure out but could not solve it
> the error:
> Error: rism>0 is incompatible with periodic boundary conditions.
> Error: To use this method set IFBOX in the PRMTOP file to 0.
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Received on Fri Aug 07 2020 - 07:30:03 PDT
