[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

[Justin A. Lemkul]

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.
> 

http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

> 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 
creates.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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