[gmx-users] problem

[Alex]

Actually, I'd like to know, too. I keep seeing this warning for systems
that are fully described in their topologies and all parameters
appropriately present in ffnonbonded, etc, i.e. everything passes grompp
and runs perfectly fine. I never really paid much attention to this
warning, thinking that gmx solvate has its own way of looking things up
elsewhere, but an explanation would be nice. I searched the list, but only
found reference to the -shell option, which I am not using.

What's happening?

Thanks,

Alex


On Sat, Sep 22, 2018 at 12:14 AM AKANXA TIWARI <akanxatiwari24 at gmail.com>
wrote:

> hello
> 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.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> 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
> (topol.top)
>
> 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
> Beefheart)
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