[AMBER] NMOD is not running for MM PBSA

From: Santanu Santra <santop420.gmail.com>
Date: Fri, 25 Jan 2019 12:50:12 +0530

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.

Santanu Santra


AMBER mailing list

Received on Fri Jan 25 2019 - 00:00:02 PST
Custom Search