[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 15 12:40:31 CET 2011
arun kumar wrote:
> 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 tutorial
> 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....
The problem is not the reliability of Gromos96, but the reliability of PRODRG.
Please read the paper linked from
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to understand why
you should almost certainly never use the charges and charge groups that PRODRG
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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