Dear All,
I am trying to calculate binding energy of protein-carbohydrate
complex by using MM-PBSA method inbuilt in amber. For this we have taken
amber forcefield simulated in amber12 package. When we are calculating
binding energy by PB & GB method , it's successfully generating the result,
but while we are trying to calculate by nmod method, it is giving some
error as follows
CalcError: /home/XXXX/software/amber12/bin/mmpbsa_py_nabnmode failed with
prmtop complex_uprt.prmtop!
we have generated all the four types of prmtop( receptor, ligand
complex_vacuum, complex_solvated) but could not able to find the source of
error.Also we have used mbondi2 version for N-H modifieradius.
Any kind of suugestion is highly apprecited.
input file for nmod is attached herewith.
Thanks in advance.
regards
Santanu Santra
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Received on Fri Jan 25 2019 - 00:00:02 PST
