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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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