VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Jun 06 2007 - 10:07:13 CDT

Jan:
My second reply to your message.

As I have a computational program that affords ESP
RESP and CRESP charges reliably for a molecule that
was cut into fragments and recomposed (with a check of
dipole moments), is it possible to insert manually
into paratool the charges so obtained (instead of
computing them again by the procedure that you
suggested)? Of course, I have a graphic control of
which is which about all atoms, hydrogens included
(and a control of the conformation). I am talking of
molecules of 50-300 atoms, so that the manual transfer
would not be too difficult.

My computational program does not allow using the
various FF, such as GAFF, which of my main interest.
With the partial charges manually transferred as above
said, I would like to try to go further on with
VMD/NAMD using GAFF.

Incidentally, I got a bit confused by the second page
of your "Paratool User's Guide", i.e., the way you
decomposed aspartate. What I see is acetate and
glycine as components.

Thanks

francesco pietra

--- 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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