[gmx-users] gmxpbsa -protein-DNA

Urszula Uciechowska urszula.uciechowska at biotech.ug.edu.pl
Tue Oct 20 14:43:06 CEST 2015

Dear all,

I am trying to run gmxpbsa for my protein-DNA complex. The problem is that
I am getting very high energies in the final MMPBSA file:

Number of frames                =          20

Overall Coulombic               =        -24244.152    +/-    38.102   kJ/mol
Overall Lennard-Jones           =        -793.343    +/-    62.428   kJ/mol
Polar solvation                 =        30532.547    +/-    21.265   kJ/mol
Npolar solvation                =        -90.506    +/-    0.136   kJ/mol

Polar contribution              =        6288.300       kJ/mol
Non-polar contribution          =        -883.849       kJ/mol

Final Value                     =        5404.546    +/-    57.935   kJ/mol

The input file:


root      gmxpbsa

multitrj      n

run                     1                               #options: integer

RecoverJobs            y                                #options: y,n

Cpath                  /usr/local/common/bin
Apath                  /usr/local/common/bin
Gpath               /usr/local/common/share/gromacs4.6.3/bin


use_topology            n                               #options: y,n
        itp_receptor  trp.itp
        itp_ligand    ben.itp
use_nonstd_ff           n                               #options: y,n
ffield                 6


complex                 complex
receptor                protein
ligand                  ligand

skip                    25                             #options: integer
min                     y                               #options: y,n

double_p                n                               #options: y,n


coulomb                  coul                     #options: coul,gmx

linearized              n                               #options: y,n
precF                   1                               #options: integer
temp                    300
bcfl                    sdh                             #options:
pdie                    4                               #options: integer,
usually between 1 and 20


cluster                 n                             #options: y,n
Q                       ...                                     #necessary
only if cluster="y"!!

mnp                     1                             #options: integer

pdf                     n                               #options: y,n


cas                     n                               #options: y,n

I have laredy try to change the "pdie" value in the input file but I did
not get lower energies. I have also asked on gmxpbsa forum.
My complex consits of protein and dna.

Thank you in advance for any sugetions.

best regards

University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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