[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
arunjones.kumar89 at gmail.com
Tue Nov 15 12:24:15 CET 2011
i had a problem while running the of protein-ligand complex simulation, in
which i have generated the ligand toplogy by using online Prodrg server and
iam using gromos 96.1froce field.
there was an note and an error during minimization
NOTE 2 [file trp.top]:
The largest charge group contains 15 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Analysing residue names:
There are: 223 Protein residues
There are: 1 Other residues
There are: 25853 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
Number of degrees of freedom in T-Coupling group rest is 161838.00
Largest charge group radii for Van der Waals: 0.790, 0.356 nm
Largest charge group radii for Coulomb: 0.790, 0.399 nm
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (1.188798) is larger than
i am using the mdp file the one that i copied from gromacs protein-ligand
can any one please explain these errors so that i can go farward in my work.
and i have a doubt, as there are other updated forcefields, how much
reliable is the gromos 96 ff....
Arun Kumar Somavarapu
Dr. Prasanna's lab
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