Subject: summary on Convert 2d to 3d in batch mode

From: Jianquan Chen <[email-masked]>
Date: Sun, 21 Jul 2002 12:10:30 -0400 (EDT)

Date: Tue, 4 Jun 2002 12:11:52 -0400 (EDT)
From: Jianquan Chen <[email-masked]>
To: [email-masked]
Subject: CCL:convert 2d to 3d

Hi,
I need to convert thousands of 2d sdf file to 3d mol2 files and add
charges. But I met a problem. Concord and Corina is too expensive. Concord
is built in the alchemy2000 that is not very expensive. I have a
question before I buy Alchemy2000. Can I run  Alchemy2000 in batch mode? I
mean, can I use alchemy2000 to convert thousands of 2d file to 3d
automatically.

Thank you in advance.

jianquan chen

A>>>From: Anselm Horn <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Conversion + charges

Hi,

some time ago, we computed the complete Maybridge database (ca. 53.000
compounds) using semiempirical MO-theory (with geometry optimization)
starting from 2D structures. We used Corina for the conversion step,
because it
may easily used in batch mode. So, this is my recommendation.

Concerning your charge problem:
If you just neeed *any* charges, you could also try Gasteiger-Marsili.
Unfortunately, I don't know, if there's a free tool around to calculate
those.
If you want to do that with Mopac, you simply do a single energy
calculation -
add keyword 1SCF to the keyword line.
Although Dave Gallagher told you of the new Mopac features, I guess that
you
use the old but free version of Mopac. There is no linear scaling
technique
implemented in that
version. So, how many molecules (which size) do you intend to compute?

Regards,
B>>>From: Karl Irikura <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Re: CCL:convert 2d to 3d

Hi Jianquan.  I don't know what Concord is, but I've used Alchemy2000
to convert 2D MOL files to 3D in batch mode.  It's a good idea to
inspect the final 3D structures, especially if stereochemistry is
important.  I did this a few years ago for a few thousand structures
(for the NIST WebBook, webbook.nist.gov), including geometry
optimization at the PM3 level.

Good luck!

Karl I.
C>>>From: [email-masked]
To: Jianquan Chen <[email-masked]>
Subject: Re: CCL:convert 2d to 3d

Jianquan-

Are you really at rutgers?  Are you working on academic pursuits without
ties to industry?  If so, our software (omega does 2d sdf to
multi-conformer (or single conf) 3dmol2 and we also have gasteiger
charges etc) is free to academics working on academic projects.

www.eyesopen.com

Cheers,
Geoff
D>>>From: Wolf-Dietrich Ihlenfeldt <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Re: CCL:convert 2d to 3d

Hello,

I suggest you talk to the CORINA people directly. If you are at an
university, I am sure things can be arranged. As a starter, there is a
free email batch service (send your structures by email and get the
structures back overnight) somewhere at www2.ccc.uni-erlangen.de/services/

---

From: Jianquan Chen <[email-masked]>
Date: Sun, 21 Jul 2002 12:14:08 -0400 (EDT)

original question is:
Hi,
I need to add charge to thousands of molecules. MOPAC is free but slow and
sometimes  changes the moleucular structure. I don't know how MOPAC
works. I have 2 questions.
Can I run MOPAC without optimizing the molecular
structure?
Is there any way to accelate MOPAC? I don't need very accurate charges.

Thanks a lot for any response.

Jianquan Chen
Hi Jianquan

A>>>>> Reply From David Gallagher, Fujitsu
1.      MOPAC can run just an "SCF" which does not change the geometry.
This is the fastest way to get partial charges.

2.      The new linear-scaling versions of MOPAC can calculate up to
20,000
atoms in just a few hours on a Windows desktop computer. With "MOPAC
2002",
an SCF on a 641 atom protein takes about 3 minutes on a 1000 MHz Pentium
III. There is more information at
http://www.cachesoftware.com/mopac/index.shtml

David Gallagher, Fujitsu
B>>>>Reply From David Gallagher, Fujitsu
1.      MOPAC can run just an "SCF" which does not change the geometry.
This is the fastest way to get partial charges.

2.      The new linear-scaling versions of MOPAC can calculate up to
20,000
atoms in just a few hours on a Windows desktop computer. With "MOPAC
2002",
an SCF on a 641 atom protein takes about 3 minutes on a 1000 MHz Pentium
III. There is more information at
http://www.cachesoftware.com/mopac/index.shtml

David Gallagher, Fujitsu

C>>>>From: Jolanta Latosinska <[email-masked]>
Subject: Re: CCL:calculate charge using MOPAC

Dear Chen,
You can run one scf within mopac package.
You should type "0" instaed of  "1" after each parameter.
Concerning the speed - try more recent version.
JL

D>>>From: Anselm Horn <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Conversion + charges

Hi,

Regards,
E>>>From: "Thomas [iso-8859-1] Hnbner" <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Re: CCL:calculate charge using MOPAC

Hello,

your first question about doing charge calculations in Mopac without
optimizing has already been answered earlier, although I would not really
recommend it.

A faster method to calculate charges is the one called Gasteiger, which
is for example implemented in the Vega package among others like Insight,
Sybyl e.a.. A new release of Vega was just announced on CCL by Giulio
Vistoli a few messages earlier, see also  http://users.unimi.it/~dd.
Together with Babel you should be able to come from almost any file
format and generate Gasteiger charges for your molecules.

The ViewerLite from Accelrys can calculate charges as well, probably also
via a Gasteiger look alike.

One word of caution though, Gasteiger is mainly applied to standard
organic/medicinal molecules, and thus probably only validated for that
class of compounds. A fuzzy clasification, I know ;-). Once you leave the
field of standard chemistry, you should use a quantum chemical method
like Mopac, or if it gets even worse you have to revert to first
principle methods like DFT or HF, as in Gaussian (commercial) or Gamess
(free).

Bye

Thomas
F>>>From: [email-masked]
To: [email-masked]
Cc: [email-masked]
Dear Jianquan,

You should take a look on the BatchMan program:
http://web.univ-orleans.fr/SCIENCES/ICOA/batchman/index.html

BatchMan is a FREE graphic interface to Mopac, Gamess and Babel,
mainly oriented to handle a large number of structures (batch mode).

With the use of one SCF step in the mopac calculation (chose
optimization: none
in the Mopac keywords interface), you will
be able to treat easily several thousand of structures without
the need to know how Mopac works.

Hope that helps.

Regards,
Eric.	
G>>>From: Juan Alexander Padron Garcia <[email-masked]>
To: Jianquan Chen <[email-masked]>
Subject: Re: CCL:calculate charge using MOPAC

    [ The following text is in the "iso-8859-1" character set. ]
    [ Your display is set for the "US-ASCII" character set.  ]
    [ Some characters may be displayed incorrectly. ]

Dear Chen:

Yes, you may. To skip the geometry optimization just add the keyword
"1SCF".
The
acceleration is not that easy and is not required if you use the 1SCF
command.
Sometimes the use of the Eigenvector Following (EF keyword) reduce the
calculation times. But a simple command line like "1SCF PM3 MMOK
GEO-OK" should
work.

Additionally, if you need help making a batch of thousand structures I can
give
you an small MSDOS program I wrote that do so automatically.