VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu May 24 2007 - 02:48:06 CDT

Jan:
Thanks. As soon as the Linux-Debian amd64 machine is
free I'll try to install VMD. I do not expect anything
easy. We are used at climbing, and that way perhaps
also aiding developers with specific issues.

As to GAFF, I wrongly posed the question to VMD, I
should have investigated at NAMD. Perhaps the answer
is already on the web.

Regards
francesco

--- Jan Saam <jan.saam_at_charite.de> wrote:

> Dear Francesco,
>
> your questions were not improper at all, I have just
> been *very* busy with
> other things so that I didn't find time to answer
> earlier...
>
> Regarding question 1:
> In paratool you can import an ascii file containing
> the cartesian Hessian
> using the menu: Hessian->"Import raw cartesian
> Hessian". You can compute
> the essian with your favourite QM package and
> convert it into the
> following form:
> For a 10-atom molecule you should have 30 lines each
> containing 30 values.
> Since the Hessian is symmetric you may also omit the
> upper diagonal.
>
> Before you load the Hessian you must provide
> paratool with the according
> optimized geometry. By default paratool expects a
> gaussian logfile but you
> can also load a pdb instead.
>
> Note that Paratool is in an early state of
> development thus somoe
> important features are still incomplete.
>
> Regarding question 2:
> Except for the paratool plugin VMD does not
> understand force fields at
> all. VMD is a viewing and analyzing tool and doesn't
> need the FF info
> (yet*). NAMD is a MD simulation engine that
> understands CHARMM, Gromacs
> and AMBER parameters. I'm not sure about GAFF but I
> think the files are in
> the same format as AMBER so NAMD should be able to
> handle it.
>
> * I agree that there are many desireable application
> where it would be
> beneficial if VMD understood force fields. We are
> working on this...
>
> I hope this helps,
> Jan
>
>
> ---------------------------
> Jan Saam
> Institute of Biochemistry
> Charite Berlin
> Monbijoustr. 2
> 10117 Berlin
>
>
> +49 30 450-528-446
> saam_at_charite.de
>
> > Either I am bothering developers and subscribers
> with
> > improper questions, or paratool/gaff are not in
> common
> > use at vmd, so that noone is able to answer.
> Though,
> > more and more problems can't be attacked with
> > classical MD with parameters for only
> > nucleotides/proteins/carbohydrates/"lipids".
> >
> > Thus, I posed two questions in a three weeks
> period
> > that remained unanswered. Here again:
> >
> > 1)Is it possible to provide (manually) the data
> > paratool needs using a QM code that is neither
> > Gaussian or Gamess?
> >
> > 2)If I understand, the GAFF FF can be imported
> into
> > VMD. Correct?
> >
> > That would save me the time of installing NAMD/VMD
> to
> > try myself, perhaps to learn that the answer is NO
> to
> > question (1), a problem that I could not
> circumvent
> > otherwise.
> >
> > Thanks
> >
> > francesco pietra
> >
> >
> >
> >
>
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