[ghemical-users] Re: [ghemical-devel] Re: Ghemical

Tue Apr 4 03:41:43 EDT 2006

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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