VMD-L Mailing List

From: Lisa Brown (lisa.brown2009_at_gmail.com)
Date: Tue Mar 31 2009 - 15:25:00 CDT

Hi Jan, and VMD users,

I am a new paratool user. Sorry for asking so many questions.
I emailed before asking about a good tutorial, but still I did not get
a reply. I tried UG by myself since I like to learn this.
I have few questions came up working with the user’s guide, about

1.The pdb of the “parent molecule”: it includes ONLY if there is a
covalent bond or a complex coordinate bond.
If there is an electrostatic interaction (similar to electrostatic
interactions of receptor-ligand ), Do I need to consider PARENT
MOLECULE?

2.Selecting most similar atom types: Is it enough to consider the
chemical nature of the next neighboring atoms (total of 2 atoms in
both sides) or more than that?

3.Improper internal coordinates: How to add IC for improper? (
specially for aromatic rings)

4.“Known atom types”: If all “atom types” are known then it will
generate the charges in the topology file (if created before QM
calculations), if one atom type is unknown it won’t generate charges
and have to do QM calculations? I need to confirm this.

5.I guess, the auto generation of Input files for GAMESS is still
under development (not in VMD 1.8.6). How can I manually generate
them? (I have access to GAMESS only)Or can I use Gaussian input file?

6.I want to confirm followings, (since I am stuck at the QM calculations)

a.After QM calculations: Can CHARMM style charges be determined by
selecting “Determine CHARMM type charges” under “Charges” in paratool
main menu?

b.The ‘parameter refinement’ is done by, selecting Edit --> refine 1-4
non-bonded interactions?

c.the final steps: File --> write topology and write parameter,
followed by write psfgen input file and run psfgen
Can the above things do automatically as described?

7.Finally, NAMD dynamics. Or are there any other important things
because of “to be continued..” at the end of the UG?

8.Do you have any published work on paratool as a reference other than
Saam et al 2007 PNAS?

Thank you so much for your attention and time.
Lisa