[ghemical-devel] Re: Ghemical

Tue Apr 4 08:08:00 EDT 2006

hi tommi
thank you for taking care

i understand the problem of resources hope will be found
francesco
On Tuesday 04 April 2006 09:41, Tommi Hassinen wrote:
> On Mon, 3 Apr 2006, Francesco Pietra wrote:
> > hi geoff
> > thank you for taking care of my problems. hope the discussion can help
> > others too. see below
>
> Hello,
>
> it's good to know about user's problems and needs. BTW some weeks ago I
> opened a new mailing list ghemical-users for this purpose ; therefore I
> send (cross-post?!?) this mail to this new (so far quiet) list as well.
> See here for more information about the list:
>
>  	http://bioinformatics.org/mailman/listinfo/ghemical-users
>
> On the other hand, there is also a question where the resources come for
> implementing new important features. At least I don't automatically have
> them, that's for sure. In fact I haven't had time to properly maintain
> even the those MPQC features we currently have.
>
> Regards,
>
>  	Tommi
>
> > On Monday 03 April 2006 16:50, Geoffrey Hutchison wrote:
> >> Ciao Francesco,
> >>
> >> I'm forwarding your message to the Ghemical mailing list and will
> >> make a few comments. I certainly appreciate your feedback -- it's
> >> good to hear from users. (By the way, what do you describe as "large"
> >> molecules? 40-50 atoms? More?)
> >
> > current problems with natural products made of 44 carbons plus 5 oxygens,
> > 2 nitrogens and hydrogens to fulfill valency.
> >
> >> I agree with the difficulty in running DFT jobs under MPQC in
> >> Ghemical right now. One workaround, obviously is to use the "export"
> >> feature to write an MPQC input file directly. This has the advantage
> >> of running a batch of MPQC jobs on another computer (which is what I
> >> usually do with GAMESS or MPQC).
> >
> > yes, this is just what i do with mpqc, using internal or cartesian
> > coordinates from the MM minimizer output to input ab initio.
> >
> >> You mention "lack of a modern molecular mechanics program" for
> >> "reasonably minimized conformers." I'm not sure what you mean -- I've
> >> done Monte Carlo conformer searching using Ghemical and found pretty
> >> reasonable conformers. In fact, I think the MC searching algorithm in
> >> Ghemical is pretty good -- often finding better candidates than other
> >> programs. While Ghemical doesn't offer tons of MM force fields, I
> >> think its MM parameters are pretty decent.
> >
> > i never used montecarlo before because i tought it is for biopolymers
> > like proteins; my molecules are of the organic type: no repeating units,
> > multiple rings, bridgeheads, and, keypoint, unsaturated bonds. in fact, i
> > had a brief trial with my molecules by montecarlo on ghemical but i was
> > unable to get a map of local minima (i had established by other MM ways a
> > large number of minima witin a 1.5 kcal/mol window)
> >
> >> I'm not sure when the Ghemical-2.0 release will happen, but I suspect
> >> that Michael Banck will try to get a Debian package fairly soon --
> >> he's one of the developers of Ghemical too.
> >
> > i look forward to installing the new version of ghemical.
> >
> > finally, i hope that my criticism was not taken by anyone as adverse
> > criticism; when i use the word "criticism" i always mean "constructive
> > criticism"; the problem is if it may be really constructive....
> >
> > best wishes
> > francesco
> >
> >> Best regards,
> >> -Geoff
> >>
> >>> version installed on my debian testing/unstable is 1.91-2.
> >>>
> >>> making clear that i am a natural product chemist, therefore
> >>> interested in
> >>> computation for "large" organic molecules, the problems i noticed,
> >>> and which
> >>> let me set aside ghemical for the time being, are:
> >>>
> >>> --lack of input to mqcp for DFT calculations (many body
> >>> calculations cannot be
> >>> carried out on my molecules; choosing a restrited basis set, they are
> >>> useless);
> >>>
> >>> --lack of a modern  molecular mechanics program to input to mqcp
> >>> reasonably
> >>> minimized conformers.
> >>>
> >>> although i am quite new to mqcp i am investing on it (to escape
> >>> institutional
> >>> restrctions for cpu time, i am building at home a workstation based
> >>> on a
> >>> couple of dual core amd64 opterons on a tyan k8we mainboard and a
> >>> couple of
> >>> hd raid1 300GB each and i plan to feed it debian testing). i was
> >>> attracted by
> >>> the native conception of mqcp for parallel calculations, so that i
> >>> am even
> >>> planning to change to it on mainframe. i have experimented a few
> >>> calculations
> >>> on a amd athlon 1ghz and found them absolutely faster than on
> >>> gamess (i do
> >>> not know gaussian which is used by my colleagues: i believe that
> >>> carrying out
> >>> molecular calculations blindly on proprietary software is a waste
> >>> of time)
> >>>
> >>> that said, it will take time before i am ready to carry out
> >>> calculations on
> >>> the new workstation. however, i am extremely interested in the new
> >>> version of
> >>> ghemical. certainly an input to ab initio from a graphical
> >>> interface relieves
> >>> fro the hardest problems if the molecule is large. it would be
> >>> great if you
> >>> can provide me a debian package in advance (please the package
> >>> because these
> >>> trials are during spare time: the burden of normal duties is heavy
> >>> indeed and
> >>> compilations normally take time).
> >>>
> >>> finally, thank you very much for contacting me. it was great pleasure
> >>>
> >>> francesco
> >>>
> >>> On Friday 31 March 2006 02:28, you wrote:
> >>>> Dear Francesco,
> >>>>
> >>>> While there are other open QM programs, I can certainly understand
> >>>> your choice of MPQC. Have you checked out the free program Ghemical?
> >>>> The current development version for v2.0 is quite good -- I use it
> >>>> for molecular mechanics and conformational analysis daily. I'd be
> >>>> glad to send you a "snapshot," or you can wait a few weeks for v2.0
> >>>> to be released.
> >>>>
> >>>> http://www.uku.fi/~thassine/ghemical/
> >>>>
> >>>> (Incidentally, Ghemical uses Open Babel for file import/export,
> >>>> although pieces exist to run MPQC and MOPAC directly, and support for
> >>>> GAMESS-US has been contributed recently.)
> >>>>
> >>>> Cheers,
> >>>> -Geoff
> >>>>
> >>>> On Mar 29, 2006, at 2:36 PM, Francesco Pietra wrote:
> >>>>> preoccupied because i am investing in mpqc for my computational
> >>>>> future,
> >>>>> abandoning other software.
> >>>>>
> >>>>> the generation of unambiguous coordinates for all atoms of a
> >>>>> complex organic
> >>>>> molecules (from 20 to 40 carbons, plus all other atoms, IDROGENS
> >>>>> INCLUDED) is
> >>>>> what i need to build an input for ab initio computation. and the
> >>>>> generation
> >>>>> can only be from graphics, because it is only the graphics that
> >>>>> allows
> >>>>> debugging in case of complex molecules (unless one aims at doing
> >>>>> that by
> >>>>> inspection of dreiding model and with the aid of mechanicall metric
> >>>>> tools,
> >>>>> which, however, will never work). and the input to mpqc must be
> >>>>> from well
> >>>>> minimized conformers through a modern force field, otherwise there
> >>>>> is no hope
> >>>>> for any ab initio method.
> >>>>>
> >>>>> which talk is not to disregard the work that is being done around.
> >>>>> difficult,
> >>>>> heavy work. but the competion of proprietary software is severe.
> >>>>> most of this
> >>>>> creates only illusion, but the atomic coordinates are generated
> >>>>> accurately.
> >
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