arun kumar arunjones.kumar89 at gmail.com
Tue Nov 15 12:24:15 CET 2011

Dear friends,

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 Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
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
  rlist (1.000000)

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
Navi Mumbai-410210
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