VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Oct 16 2015 - 09:58:51 CDT

This new tab allows you to input the MOL2 (or PDB) file that was submitted to the CGenFF Program (formerly known as ParamChem) and the stream file (STR). ffTK will parse the data and show the parameter information in the GUI. From there you can write out a PSF+PDB file pair and/or a parameter file (PAR) that can be used as a good starting point for parameterization.

* A note regarding a bug in the current parsing of CGenFF Program STR files: if the file uploaded to the CGenFF Program web server contains invalid atom names (i.e., duplicates), the atom names will be changed to unique value in the returned stream file. ffTK currently parses this incorrectly, so make sure that the uploaded files are valid! (I’m hoping to fix this soon).

Currently, the best way to handle impropers is to assign them by analogy and separate them into their own parameter file, which should be included as an “Associated Parameter File” during the optimizations.

Regards,
Christopher Mayne

> On Oct 16, 2015, at 3:01 PM, fvlieffe <Francois.Van.Liefferinge_at_ulb.ac.be> wrote:
>
> Hi all,
>
> first I would like to thank you for your help, I just finish to parametrize my first molecule.
>
> but I have still 2 questions:
>
> - there is a new option in the "built par" menu, wich is called "Prepare Parameterization from CGENFF Program Output" and before starting
> using FFTK, I tried the all CGENFF procedure. So I have the output of CGENFF and I create a par file from it. So the question is: how can I use it
> in the FFTK process? can I add it when parameters files (both in progress or pre-defined) are asked?
>
> - I know that FFTK does not include a tool for Improper, but can I assignate Improper by analogy (example: between existing piridine and custom
> aminopyrimidine)?
>
>
> thank you
>
>
> regards
> --
> Van Liefferinge François
> Phd Student in Chemistry
> S.F.M.B., Université Libre de Bruxelles
> Campus Plaine CP 206/2
> Bâtiment BC, local 1C4.107
> Blvd. du Triomphe
> B-1050 Bruxelles
> BELGIQUE
>