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 - 07:00:02 PDT
