From J_BROWN@uvmvax.uvm.edu Thu Feb 18 03:45:00 1993 Date: Thu, 18 Feb 1993 08:45 EST From: J_BROWN@uvmvax.uvm.edu Subject: MM2 local minima and one possible solution To: chemistry@ccl.net Message-Id: <01GUV0D38TF4002XKL@uvmvax.uvm.edu> Harry C. Johnson IV writes: > In testing our geometry optimization program that utilizes > genetic algorithms, we were able to obtain a lower energy conformation > than MM2. This is not too suprising, however, when we gave our new > geometry to MM2, it calculated an initial energy of ~9.44 and ended > with a final energy, after _minimization_, of ~10.05!! I was just > curious why this might be? Any ideas? I have found that MM2 (87) will minimize to a local minima with a "rough" starting geometry. This is especially true with long alkyl side chains and benzyl R groups. In dibenzylmethylamine, MM2 (87) will minimize a rough geometry until the benzyl groups come within the ring proton van der walls radius of each other, then the energy goes up, and the minimzation stops (as is should). I will often take that final geometry and check it to see if a R group has fully minimized or if it has gotten "stuck" in a local minima. From topper@haydn.chm.uri.edu Thu Feb 18 05:57:25 1993 Date: Thu, 18 Feb 93 10:57:25 -0500 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9302181557.AA20410@haydn.chm.uri.edu> To: chemistry@ccl.net Subject: Re: MM2 local minima and one possible solution Re: HC Johnson IV's note: > In testing our geometry optimization program that utilizes > genetic algorithms, we were able to obtain a lower energy conformation > than MM2. This is not too suprising, however, when we gave our new > geometry to MM2, it calculated an initial energy of ~9.44 and ended > with a final energy, after _minimization_, of ~10.05!! I was just > curious why this might be? Any ideas? Perhaps all three minima are local minima? Or perhaps only the first two? You'll never know unless you somehow sample the full N-dimensional space....maybe this is a job for simulated annealing? :-) Seriously, gradient search methods are never guaranteed to find anything other than local minima. I don't know what brand of algorithm the other method is, but....let the buyer beware. -Robert ******************************** * Robert Q. Topper, Ph.D. * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * rtopper@chm.uri.edu OR * * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** From jle@world.std.com Thu Feb 18 07:50:05 1993 Date: Thu, 18 Feb 1993 12:50:05 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199302181750.AA09614@world.std.com> To: chemistry@ccl.net Subject: Question about PDB format Large molecule folks... I've seen a lot of PDB formats in my time, but recently I've seen one that looks unusual. The "standard" format seems to have a 2 character atom label field (such as " C" and "CA") and a 2 digit index field. Ok... Recently, I've been sent a file with the following functional group: 1H24 | 2H24--N24-- . . . rest of molecule | 3H24 The obvious convention is that there are the three H's on N24. However, it places a number in the atom label field. I thought the PDB "legal" format was somewhat strict (can you say F77?) on column layouts and contents. Am I missing something (and is this legal)? Or am I seeing yet another custom extension to the malleable PDB format? Joe Leonard jle@world.std.com From ZURAW%athena@leia.polaroid.com Thu Feb 18 12:06:31 1993 Message-Id: <199302182205.AA00284@oscsunb.ccl.net> Date: 18 Feb 1993 17:06:31 -0500 (EST) From: ZURAW%athena@leia.polaroid.com Subject: 3D->2D drawing summary To: CHEMISTRY@ccl.net Dear Netters, I posted the following question a couple of weeks ago: > "I am looking for a program that will take 3D coordinates >and connectivity information and output a 2D drawing. I have >a few hundred compounds which I have minimized with either Sybyl or >CAChe from which I would like to create a data base that is easy to >browse through visually. I'm looking for a substitute for manually >redrawing all of the compounds with Chemdraw. I do not want a >program that will generate a projection of the 3D drawing." Many thanks to those 14 people who responded with suggestions. I have not yet found the ideal solution, but when I do I'll be sure to let everyone know. The following is what I have found: *** Sybyl 6.0 (Tripos) molecular spread sheet option creates 2D drawings from 3D structures using templates. I've tried this and it does work. The spread sheet runs rather slow on my SGI 4D210/16MB machine and the only way of creating a hard copy output seems to be a screen dump. The 2D drawings are far from perfect, but are better than a projection. Tad Hurst from Tripos informed me that the Sybyl/Unity software enables you to customize the 3D to 2D conversion to improve the 2D drawings. ** ISIS Draw (MDL) does not yet convert 3D molecular structures to 2D drawings, but they say the next release (early summer) will have this feature. ** ChemOffice, ChemFinder, Chem3D +, ChemDraw +, etc. None of the Cambridge Scientific packages will take 3D structures and convert them to 2D (non-projection) drawings. They are working on this option, but they do not have a release date planned. ** Consystant/Chemeleon (Windows and DOS), by Exographics (PO Box 655, West Milford, NJ 07480 USA, Tel 201-728-0188) I have not yet confirmed that this package can do the 3D to 2D conversion, but the person that I talked to there was convinced that it would. When I get further information or a copy of the program I'll post the information to the list. **** It appears that for now, if I want "publication quality" 2D drawings (not ORTEP drawings or projection drawings) of molecules I have generated with Sybyl or CAChe, I'll have to redraw them ChemDraw. Since ChemDraw will output SMILES notation as well as a connection file, it appears the smart thing to do would have been to draw everything with ChemDraw and convert the drawings to Sybyl and/or CAChe files. Regards Michael Zuraw From autodesk!autodesk.com!raw@fernwood.mpk.ca.us Thu Feb 18 06:22:08 1993 Date: Thu, 18 Feb 93 14:22:08 PST From: raw@autodesk.com (Robert A Whiteside) Message-Id: <9302182222.AA10968@miki.YP.acad> To: jle@world.std.com Subject: Re: Question about PDB format I have seen this kind of thing before, many file from the Brookhaven database do this kind of thing. Atom names have a maximum of 4 characters, and the atomic symbol must be right-justified in the first two. Thus, the heavy atom in the example is names " N24" (significant leading space). The idea for naming hydrogens, apparently, is that a hydrogen gets named by giving it the postfix of the heavy atom to which it is attached. Thus, the hydrogen attached to this " N24" should be called " H24". The problem, now, is how do we differentiate the three hydrogens? Can't call it " H241", since that has too many characters. Somebody decided that, since there's a leading space (just going to waste), hydrogen names could wrap around, giving "1H24". Sigh. (Can you say FORTRAN?) I understand that the Brookhaven folks are working on a more sensible format... --Bob Whiteside >> Date: Thu, 18 Feb 1993 12:50:05 -0500 >> From: jle@world.std.com (Joe M Leonard) >> Sender: chemistry-request@ccl.net >> Precedence: bulk >> >> Large molecule folks... >> >> I've seen a lot of PDB formats in my time, but recently I've seen one that >> looks unusual. The "standard" format seems to have a 2 character atom >> label field (such as " C" and "CA") and a 2 digit index field. Ok... >> Recently, I've been sent a file with the following functional group: >> >> 1H24 >> | >> 2H24--N24-- . . . rest of molecule >> | >> 3H24 >> >> The obvious convention is that there are the three H's on N24. However, >> it places a number in the atom label field. I thought the PDB >> "legal" format was somewhat strict (can you say F77?) on column layouts >> and contents. Am I missing something (and is this legal)? Or am I seeing >> yet another custom extension to the malleable PDB format? >> >> Joe Leonard >> jle@world.std.com >> >> >> --- >> Administrivia: This message is automatically appended by the mail exploder: >> CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator >> OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net >> CHEMISTRY-SEARCH@ccl.net --- search the archives, read help.search file first >> --- >> >> From fisher@scripps.edu Thu Feb 18 09:02:32 1993 Date: Thu, 18 Feb 93 17:02:32 PST From: fisher@scripps.edu (Cindy Fisher) Message-Id: <9302190102.AA21504@crystal.Scripps.EDU> To: chemistry@ccl.net Subject: Re: Question about PDB format Joe, That's what I've heard is the "official" format for hydrogen names in the PDB. Strange... =========================================================================== Cindy Fisher Department of Molecular Biology--MB4 The Scripps Research Institute 10666 North Torrey Pines Road La Jolla, CA 92037 E-mail to: fisher@scripps.edu From vincent@retina.chem.psu.edu Thu Feb 18 16:03:23 1993 Date: Thu, 18 Feb 93 16:02:00 -0500 From: vincent@retina.chem.psu.edu (Jim Vincent) Message-Id: <9302182102.AA26568@retina.chem.psu.edu> To: CHEMISTRY@ccl.net Subject: Parallel AMBER Is anyone working on porting AMBER to parallel machines of any type? I have read the recent summary of programs that have been ported to various machines but have seen nothing concerning AMBER running in parallel either on shared or distributed memory machines. If you are working on this could you drop me a note? If I receive any replies I'll summarize. Jim Vincent vincent@retina.chem.psu.edu