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
--
========================================
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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