[gmx-users] problem

AKANXA TIWARI akanxatiwari24 at gmail.com
Sat Sep 22 08:13:45 CEST 2018

i am simulating tubulin heterodimer . after giving command for solvent
adding i got a warning on screen what should i do.

Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
         based on residue and atom names, since they could not be
         definitively assigned from the information in your input
         files. These guessed numbers might deviate from the mass
         and radius of the atom type. Please check the output
         files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
-------- -------- --- Thank You --- -------- --------

Generating solvent configuration
Will generate new solvent configuration of 7x7x7 boxes
Solvent box contains 202791 atoms in 67597 residues
Removed 17799 solvent atoms due to solvent-solvent overlap
Removed 10800 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 58064 residues
Generated solvent containing 174192 atoms in 58064 residues
Writing generated configuration to 1jff_solv.gro

Output configuration contains 182636 atoms in 58902 residues
Volume                 :     1882.42 (nm^3)
Density                :     1006.94 (g/l)
Number of solvent molecules:  58064

Processing topology
Adding line for 58064 solvent molecules with resname (SOL) to topology file

Back Off! I just backed up topol.top to ./#topol.top.1#

GROMACS reminds you: "She's Not Bad, She's Just Genetically Mean" (Captain

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