VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Thu May 24 2007 - 02:26:44 CDT

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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