From ssidner@unmc.edu Tue Dec 22 02:24:55 1992 Date: Tue, 22 Dec 92 08:24:55 CST From: ssidner@unmc.edu (Steve Sidner) Message-Id: <9212221424.AA04469@molecular.unmc.edu> To: chemistry@ccl.net Subject: Re: Holiday Greetings I, for one, Jan, want to thank you for your outstanding efforts as list coordinator. This list has the highest signal/noise ratios of any list I read. My colleagues and I gain much useful information. I hope your C.V. includes chemistry@ccl.net prominently as one of your publications! May the world move a little closer to peace and prosperity in 1993, as we mind the store with one hand and grop our way to our destiny with the other. Steve Sidner Eppley Institute, University of Nebraska Medical Center From ssidner@unmc.edu Tue Dec 22 02:36:41 1992 Date: Tue, 22 Dec 92 08:36:41 CST From: ssidner@unmc.edu (Steve Sidner) Message-Id: <9212221436.AA04489@molecular.unmc.edu> To: chemistry@ccl.net Subject: Internet Want Ads Work For Me As you may recall, in early September, I posted an offering of a used ESV workstation for sale. Within 24 hours I received 20 queries, from all over the world. The University subsequently held a sealed-bid auction, sending bid invitation to all who had expressed interest. As a result, the ESV was sold to another researcher at a mutually agreeable price. The buyer got an exceptionally good price, and I was able to funnel some much need funds back into my computer budget. While some may think this is an inappropriate use of the Internet in general, and chemistry@ccl.net specifically, I think it is an outstanding use. I believe the intrusion into reader's awareness was minimal, and two scientific groups were able to achieve a very mutually beneficial exchange that would have been difficult to accomplish otherwise. This really took advantage of the "information content" on this list in a way that is unique to cyberspace. Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805, U.S.A. (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From hogue@mosquito.den.mmc.com Tue Dec 22 01:22:52 1992 Date: Tue, 22 Dec 92 08:22:52 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9212221522.AA01371@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: Taxol modelling Dear netters: Does anyone know if Taxol has been modelled? I would like to give it a try using AM1 but would like to hear from others with experience or opinions with large molecules like this. Thanks in advance. Pat Hogue From jkl@ccl.net Tue Dec 22 06:04:17 1992 From: Jan Labanowski Date: Tue, 22 Dec 1992 11:04:17 -0500 Message-Id: <199212221604.AA04845@krakow.ccl.net> To: chemistry@ccl.net, sybyl@quant.chem.rpi.edu Subject: Cartesians-->SYBYL MOL files conversion Dear Netters, Some people asked for a program which converts a table of cartesian coordinates to a SYBYL MOLfile. The program q2m will do that (sometimes you need to correct the atom types, I do not check for aromaticity and other funny bonding situations. Program also does not know about formal charges on atoms). But I found it usefull to display molecules in SYBYL when I have only cartesian coordinates (e.g. from some quantum codes). I cannot give you a source code yet, but the binaries for CRAY-YMP, SiliconGraphics, RS6000 and SUN-SPACK are available. You can only get this program via anonymous ftp. If you really need the binary via e-mail, tell me and I will send you the uuencoded version. The ftp site is: www.ccl.net [128.146.36.48]. Login in as anonymous and give you e-mail address as password. The program is located in the directory /pub/chemistry/q2m The following files are there: bin subdirectory holds binary versions for different machines: (remember to set binary transfer when retrieving these files with ftp). 158432 Dec 22 11:23 q2m.cray.ymp (CRAY-YMP) 35896 Dec 22 11:21 q2m.rs6000 (RS6000) 75072 Dec 22 11:21 q2m.sgi (SiliconGraphics) 40960 Dec 22 11:21 q2m.sun-spark (Sun-Spark) doc subdirectory has documentation: 6779 Dec 22 11:29 q2m.ascii (Plain ASCII doc) 7429 Dec 22 11:28 q2m.man (processed by nroff -man, to use with UNIX) 19822 Dec 22 11:27 q2m.ps (PostScript version to print) 5762 Dec 22 11:27 q2m.troff (troff source for a man page) test subdirectory contains a few examples: 814 Dec 22 11:39 SAXYZ-B.MOL (resulting MOL file) 901 Dec 22 11:39 SAXYZ-B.dat (cartesian coordinates) 814 Dec 22 11:39 SCXYZ-B.MOL 1092 Dec 22 11:39 SCXYZ-B.dat 376 Dec 22 11:39 SCXYZSSS-B.MOL 390 Dec 22 11:39 SCXYZSSS-B.dat 706 Dec 22 11:39 SXYZM-B.MOL 950 Dec 22 11:39 SXYZM-B.dat 319 Dec 22 11:39 runexamples (script to run the examples) Jan Labanowski Ohio Supercomputer Center jkl@ccl.net From lim@rani.chem.yale.edu Tue Dec 22 12:18:03 1992 From: Dongchul Lim Message-Id: <9212222218.AA25529@rani.chem.yale.edu> Subject: Conversion of Cartesian Coordinates to Sybyl Mol1 file type To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 22 Dec 92 17:18:03 EST Dear netters, Here's my 2 hour hack of nawk script which converts cartesian coordinates to sybyl MOL1 file type. If you don't want to bother ftp'ing previously announced q2m or need a source code, you may want to try this script, although q2m will probably generate better sybyl files. This is not tested with old awk, so it'll be safer to use nawk, mawk, gawk, etc. If your sysmtem is a BSD or its clone, you'll need to change the first line of the script to "#!/bin/nawk -f". SYS V users don't need to change it, as long as "nawk" is located at /usr/bin directory. I'll explain briefly how it works. 1. read in a line (first line is treated as title and ignored) 2. if the line consists of the data types "integer number number number", the first integer is stored in "an" array, and the following three numbers are stored in "x", "y", and "z" arrays. Otherwise, the program exits with error message. 3. continue until EOF is encountered, or filename changes. 4. print out sybyl MOL1 file. 1) construct bond list by comparing the distance of each atom pair and the sum of Bragg-Slater radii of them (multiplied by "factor"). 2) count the number of neighbors for each atom. 3) determine sybyl atom type based on atomic number and # of neighbors. 4) print out atomtype, coordinates, and bond lists 5. if there're more than one file, repeat the above procedure. As you may notice, determination of sybyl atom type is not perfect and you will perhaps have to modify the script to obtain appropriate atom types. To use this program, cut out the script from this mail and name it "c2m" (or whatever you like). Then make it executable by "chmod +x c2m". On command line, type "c2m file1 file2...", where file1, file2... are cartesian type files (the first line is assumed to be a comment). This program is provided AS IS, without any warranty, implied or expressed. -Dongchul Lim Department of Chemistry, Yale Univ. ------------------- CUT HERE ---------------------------------------------- #!/usr/bin/nawk -f # @(#) c2m - Convert cartesian coordinates to Sybyl MOL1 file # Usage: c2m file1 file2... # Author: Dongchul Lim # Department of Chemistry, Yale University, lim@rani.chem.yale.edu # Date: December 22, 1992 # Disclaimer: This program is provided "AS IS", without any warranty. # The author will not be responsible for any disters which may result from # using this program. BEGIN { OLDFILE = FILENAME; factor = 1.5; # bond tolerance factor number = "^[-+]?([0-9]+[.]?[0-9]*|[.][0-9]+)([eE][-+]?[0-9]+)?$"; integer = "^[-+]?[0-9]+$"; natoms = 0; nbonds = 0; # Bragg-Slater Radii (change values if needed) r[1] =0.35; r[2] =0.50; r[3] =1.45; r[4] =1.05; r[5] =0.85; r[6] =0.70; r[7] =0.65; r[8] =0.60; r[9] =0.55; r[10]=0.65; r[11]=1.80; r[12]=1.50; r[13]=1.25; r[14]=1.10; r[15]=1.00; r[16]=1.00; r[17]=1.00; r[18]=0.95; r[19]=2.20; r[20]=1.80; r[21]=1.60; r[22]=1.40; r[23]=1.35; r[24]=1.40; r[25]=1.40; r[26]=1.40; r[27]=1.35; r[28]=1.35; r[29]=1.16; r[30]=1.35; r[31]=1.35; r[32]=1.30; r[33]=1.25; r[34]=1.15; r[35]=1.15; r[36]=1.15; r[37]=1.10; r[38]=2.35; r[39]=2.00; r[40]=1.80; r[41]=1.55; r[42]=1.45; r[43]=1.45; r[44]=1.35; r[45]=1.30; r[46]=1.35; r[47]=1.40; r[48]=1.60; r[49]=1.55; r[50]=1.55; r[51]=1.45; r[52]=1.45; r[53]=1.40; r[54]=1.40; r[55]=1.50; r[56]=1.50; r[57]=1.50; r[58]=1.50; r[59]=1.50; r[60]=1.50; r[61]=1.50; r[62]=1.50; r[63]=1.50; r[64]=1.50; r[65]=1.50; r[66]=1.50; r[67]=1.50; r[68]=1.50; r[69]=1.50; r[70]=1.50; r[71]=1.50; r[72]=1.50; r[73]=1.50; r[74]=1.50; r[75]=1.50; r[76]=1.50; r[77]=1.50; r[78]=1.50; r[79]=1.44; r[80]=1.50; r[81]=1.50; r[82]=1.50; r[83]=1.50; r[84]=1.50; r[85]=1.50; r[86]=1.50; r[87]=1.50; r[88]=1.50; r[89]=1.50; r[90]=1.50; r[91]=1.50; r[92]=1.50; r[93]=1.50; r[94]=1.50; r[95]=1.50; r[96]=1.50; } FNR == 1 {next;} $1 !~ integer || $2 !~ number || $3 !~ number || $4 !~ number { printf("\007Cartesian format error in line %d: %s\n", FNR, $0); exit; } # read in atomic number and cartesian coordinates { if (FILENAME != OLDFILE) { printSybyl(); printf("\n"); natoms = 0; nbonds = 0; } if ($1 <= 0+0) next; # skip dummy atoms natoms++; an[natoms] = $1; x[natoms] = $2; y[natoms] = $3; z[natoms] = $4; OLDFILE = FILENAME; } END { printSybyl(); } # print Sybyl MOL1 file type function printSybyl() { # construct list of bonds for(i=1;i<=natoms;i++) { for(j=i+1;j<=natoms;j++) { if (dist(i, j) <= r[an[i]]*factor + r[an[j]]*factor) { nbonds++; bond_a[nbonds] = i; bond_b[nbonds] = j; } } } # construct list of neighbors for(i=1;i<=natoms;i++) { neighbors[i] = 0; for(j=1;j<=nbonds;j++) if (bond_a[j] == i || bond_b[j] == i) neighbors[i]++; } # print out sybyl MOL1 type file printf("%4d MOL %-40s %4d\n", natoms, FILENAME, 0); for(i=1;i<=natoms;i++) printf("%4d%4d% 9.4f% 9.4f% 9.4f\n", i, atomtype(i), x[i], y[i], z[i]); printf("%4d MOL\n", nbonds); for(i=1;i<=nbonds;i++) printf("%4d%4d%4d %4d\n", i, bond_a[i], bond_b[i], 1); printf("%4d MOL\n", 0); } function dist(a1, a2) { # get distance between a1-th and a2-th atom d = (x[a1]-x[a2])*(x[a1]-x[a2]) + (y[a1]-y[a2])*(y[a1]-y[a2]) + (z[a1]-z[a2])*(z[a1]-z[a2]) return sqrt(d) } # get sybyl atomtype of a1-th atom function atomtype(a1) { a = an[a1]; # atomic number if (a == 0) return 26; # Dummy else if (a == 1) return 13; # H else if (a == 3) return 24; # Li else if (a == 6) { # C if (neighbors[a1] == 1) return 4; else if (neighbors[a1] == 2) return 3; else if (neighbors[a1] == 3) return 2; else if (neighbors[a1] == 4) return 1; else return 1; } else if (a == 7) { if (neighbors[a1] == 1) return 7; # N1 else if (neighbors[a1] == 2) return 6; # N2 else if (neighbors[a1] == 3) return 5; # N3 else if (neighbors[a1] == 4) return 31; # N3+ else return 5; } else if (a == 8) { if (neighbors[a1] == 1) return 9; # O2 else if (neighbors[a1] == 2) return 8; # O3 else return 8; } else if (a == 9) return 16; # F else if (a == 11) return 21; # Na else if (a == 13) return 25; # Al else if (a == 14) return 27; # Si else if (a == 15) return 12; # P3 else if (a == 16) { if (neighbors[a1] == 1) return 18; # S2 else if (neighbors[a1] == 2) return 10; # S3 else return 10; } else if (a == 17) return 15; # Cl else if (a == 19) return 22; # K else if (a == 20) return 23; # Ca else if (a == 35) return 14; # Br else if (a == 53) return 17; # I else return 26; } ------------------- CUT HERE ---------------------------------------------- From m10!frisch@uunet.UU.NET Tue Dec 22 12:41:59 1992 Message-Id: <9212222325.AA16232@relay2.UU.NET> Date: Tue, 22 Dec 92 17:41:59 EST From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: cartesian to pdb format To: chemistry@ccl.net I have a small problem and was wondering if anyone out here can help me. I have been examining a series of compounds with gaussian92. I thus have these compounds expressed as their cartesian coordinates. I would like to use Sybyl to visualize these structures. Does anyone know if a program exists to convert these cartesian coordinate files into Sybyl-readable pdb files? I was hoping to obtain this program through anonymous ftp rather than my research director's research grant. Thanks! -mark zottola zottola@chemvax.chem.duke.edu The NewZMat program distributed with Gaussian 92 can write PDB files which can be read by most graphics programs, although I haven't tested Sybyl in particular. In recent revisions of G92, you can use either the -opdb or -obkv switch to NewZMat (they are synonymous). In earlier versions, and in G90, you had to say -obkv (the clearer synonym wasn't available). Mike Frisch -------