From: dalton banks (daltonius_at_gmail.com)
Date: Tue Aug 11 2009 - 15:02:13 CDT
Hi,
I need to solvate a region with a solvent that contains other molecules than
water. On the NAMD Solvate
page<http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/>,
it says the following arguments are required:
* An equilibrated, cubic box of the solvent of choice (-spdb)
* A psf file for the solvent cube (-spsf)
* A topology file for all residue types in the solvent (-stop)
* A key selection which will occur once in each solvent residue (eg.,
"name OH2") (-ks)
* The side length of the box (should be taken from the equilibration's
periodic cell (-ts)
and I have some questions about these requirements.
1) Is there a standard procedure for creating such a box?
2) I have psf files for my solvent molecules, but no top files; is there a
way to create them from the psf files?
3) What is the key selection? This is something that's the same for all
residues?
4) This is the only documentatin I could find on Solvate, and it doesn't day
much about how to use it from the command line (the tutorial doesn't help
much more either). Is there more detailed documentation somewhere?
Thanks,
Dalton
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