VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jul 23 2013 - 09:50:51 CDT

As an example, for one of the ligands that I am considering, by
setting the pyridine ring as pure aromatic and the pyrrole ring as non
pure aromatic, in my view the calculations reduce from the FFTK
suggested 17 DIH (each + and -) to two ANGL, two DIH, and 10 IMPR. If
the latter can be assigned as either default value (1.1 180 2) or
general improper torsional angle (1.1 180 2 or 10.5 180 20) the
calculations reduce by a great deal.

I am not familiar with the above procedure, however. Just a guess to
try to circumvent an unreasonably heavy task. As the IMPROPER route
was not taken, the inventors of FFTK must have their reasons.

Here to learn.

thanks

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Jul 23, 2013 at 10:12 AM
Subject: vmd-l: Fwd: FFTK scan torsions aromatics
To: vmd-l_at_ks.uiuc.edu

In the meantime I came across

*****************
From: JC Gumbart [gumbart_at_ks.uiuc.edu]
Sent: 29 June 2013 13:55
To: Darre Castell, Leonardo
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: ureybradley and impropers in ffTK

I'd like to know too! If you write some code for these functions, let us know.

In all seriousness, it just hasn't been a priority, as they aren't
nearly as important or prevalent as the other terms in the force
field.

On Jun 28, 2013, at 11:52 AM, Darre Castell, Leonardo wrote:

Hi, this is probably a naive question, but I'd like to know how to
parametrize Urey-Bradley and Improper Torsions using ffTK tool?

Thanks a lot in advance.
Leonardo
********************

May I ask what that means for the case I have prospected? That is,
what to do when there are aromatic rings? Impose impropers by analogy
to the benzene ring or do what FFTK-ScanTorsions suggests? Should the
latter be the choice, is it acceptable to calculate ScanTorsions at
RHF/6-31G*? At MP2/6-31G*, with my workstation running gamess-us
(workstation for MD, thus with unusable GPUs), I should work for a
couple of weeks 24h/24h for my complex molecule, just for
ScanTorsions.

thanks

francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Jul 23, 2013 at 9:14 AM
Subject: FFTK scan torsions aromatics
To: vmd-l_at_ks.uiuc.edu

Hope not to have missed what seems to be an obvious answer.

FFTK ScanTorsions indicates also dihedrals involving aromatic rings,
such as pyridine and pyrrole, and more exotic ones, like tropylium and
others. Is not that a matter for impropers, forcing those rings to
planarity?

thanks
francesco pietra