[gmx-users] overlaps atoms during solvation(genbox)

[Justin Lemkul]

On 8/27/12 6:47 AM, Vasumathi Velachi wrote:
> Hi
>
> I new in using Gromacs.
>
> I used genbox to solvate my solute(gold+thiols), when I am doing so the
> resultant pdb have the overlaps between water molecule and gold. This overlaps
> is due to the missing information for gold in the file "vdwdradii.dat". In order
> to avoid the overlaps shall i increase vdwd radii while solvating or shall  I
> include the vdwd radii information for gold atoms in "vdwdradii.dat" file.
>

The most straightforward solution is to add an entry for gold in vdwradii.dat. 
Make a local copy of the file in the working directory and make your modifications.

-Justin

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

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

========================================