Dear All
I need to solvate my molecule which contain gold(AU) and thiols (S,C,H,N,O) and need to add ions also. Because of the force field problem i am not able to do it using vmd. Can anybody suggest the way to do that.
Thanking you in advance.
Regards
Dear All
I need to solvate my molecule which contain gold(AU) and thiols (S,C,H,N,O)
and need to add ions also. Because of the force field problem i am not able
to do it using vmd. Can anybody suggest the way to do that.
sure you can use VMD. why not?
it is just a matter of doing a little scripting.
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal
axel.
Thanks Axel and Daniel. I will try.
Dear Daniel
I did the solvation using genbox but the problem is information for gold atom not exist in the “vdwradii.dat”. So when i did solvation the resultant pdb file have overlap[](http://manual.gromacs.org/online/dat.html)s between water molecules and gold atoms.
May I increase the vdwd radius in genbox command or should i include the vdwd information for gold atom in the “vdwdeadii.dat” ?
Thanking you in advance
Regards
Vasumathi
I’m not too familiar with or experienced with gromacs, sorry.
You should be able to get help from the mailing list for gromacs from http://www.gromacs.org/
v/r,
dc