From chemistry-request@server.ccl.net Sat Apr 7 06:59:04 2001 Received: from mailer.psc.edu ([128.182.58.100]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f37Ax3D15519 for ; Sat, 7 Apr 2001 06:59:03 -0400 Received: from pscuxc.psc.edu (unix.psc.edu [128.182.66.177]) by mailer.psc.edu (8.11.2/8.11.2/psc) with ESMTP id f37Ax3g06935; Sat, 7 Apr 2001 06:59:03 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id GAA06755; Sat, 7 Apr 2001 06:59:03 -0400 (EDT) Date: Sat, 7 Apr 2001 06:59:02 -0400 (EDT) From: Troy Wymore To: "C. Michael McCallum" cc: Subject: CCL:creating a new residue in charmm In-Reply-To: <20010406112122.A3254@onsager.cop.uop.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Mike, The page listed below is material from the workshop given at the Pittsburgh Supercomputing Center. The subjects listed below were discussed in the lectures but we do not have scripts that explicitly handle these issues; probably because in these situations each condition would be unique. There is plenty of other material on CHARMM and biomolecular simulation at: http://www.psc.edu/general/software/packages/charmm/tutorial/index.html Good luck, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center On Fri, 6 Apr 2001, C. Michael McCallum wrote: > * C. Michael McCallum (mmccallum@uop.edu) [010406 11:15]: > > > > As a follow-up to this, I see this nice page: > > http://www.psc.edu/general/software/packages/charmm/tutorial/crowley/protein_index.html > > which includes: > > * Initial decisions and analysis (N.B. Read the pdb file carefully) > > * Titratable groups > * Xray waters > * Missing residues > * bound ions and coordination complexes > * Unknown ligands and odd residues > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Which looks like a discussion that I need, but only the first subject is > linked. > > Cheers, > > Mike > -- > C. Michael McCallum | "That may be one tough nut to crack, > Associate Professor | but I am one determined > Chemistry, UOP | little squirrel" > mmccallum@uop.edu | (209) 946-2393 | fax (209) 946-2607 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Sat Apr 7 07:04:48 2001 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f37B4lD15573 for ; Sat, 7 Apr 2001 07:04:47 -0400 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id QAA72524; Sat, 7 Apr 2001 16:43:36 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id QAA12757; Sat, 7 Apr 2001 16:42:00 +0530 Date: Sat, 7 Apr 2001 16:42:00 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: "Thoms, Travis" cc: "Computational Chemistry List (E-mail)" Subject: Re: CCL:Help a Gamess newbie... In-Reply-To: <3FD2BCBD9153D41192B100C04F1FD832067E44@cranc02.cra.canon.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, It seems to me that after cs you have to leave one blank line. If still it does not fix the problem, use CS instead cs . I hope this will solve. Tapan Ghanty On Thu, 5 Apr 2001, Thoms, Travis wrote: > Greetings: > I am taking the plunge into ab-initio calculations, using Gamess US. > I have set up a trial run for gamess to work on, but to be quite honest, I > don't quite understand what sort of information it expects for symmetry > input: > > !enter comments here > ! > ! > ! > $CONTRL SCFTYP=RHF CITYP=NONE RUNTYP=OPTIMIZE EXETYP=CHECK ICHARG=0 > ECP=NONE > COORD=ZMTMPC $END > $BASIS GBASIS=N21 $END > $DATA > TRIAL RUN > cs > C 00000.0000 0 00000.0000 0 00000.0000 0 0 0 0 > C 00001.5125 1 00000.0000 0 00000.0000 0 1 0 0 > C 00001.3212 1 00123.4130 1 00000.0000 0 2 1 0 > C 00001.4253 1 00122.7597 1 00179.9998 1 3 2 1 > N 00001.1407 1 00179.8250 1 00180.0813 1 4 3 2 > H 00001.0813 1 00110.9581 1 00179.9997 1 1 2 3 > H 00001.0845 1 00110.6745 1 00300.0425 1 1 2 3 > H 00001.0845 1 00110.6746 1 00059.9568 1 1 2 3 > H 00001.0737 1 00117.3431 1 00000.0000 1 2 1 6 > H 00001.0734 1 00121.4331 1 00000.0000 1 3 2 1 > > $END > > The first time I ran this, there was nothing after CS, much like many of the > examples in the Gamess documents. The program responded, "**** ERROR > READING VARIABLE X1 CHECK COLUMN 1". I added numbers after it like > "2" (out of sheer frustration) but nothing happened. > > I then broke down and read the instructions again. They state that for "card > 3" : "For CS group, any two points in the symmetry plane." Card 4:" For CS > group, one point of the symmetry plane, noncolliner with points 1 and 2." > > To be honest, I don't know how to format the input for these "cards" > >. Can someone give me an example? > > Thanks, > > Travis Thoms > Research Associate > Canon R&D Center Americas. inc. > Telephone: 1-408-468-2864 > Facsimile:1-408-468-2810 > tthoms@cra.canon.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ************************************************************************ Dr. Tapan K. Ghanty Theoretical Chemistry Section Chemistry Division Bhabha Atomic Research Centre Trombay, Mumbai 400 085 India Phone: 550 5050, 550 5010, 550 5000, 556 3120 Extn. 2675 ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Sat Apr 7 03:41:55 2001 Received: from nmr-v.ioc.ac.ru (root@[193.233.3.213]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f377fsD13634 for ; Sat, 7 Apr 2001 03:41:55 -0400 Received: from cacr.ioc.ac.ru (val@localhost [127.0.0.1]) by nmr-v.ioc.ac.ru (8.9.3/8.9.3) with ESMTP id LAA10673 for ; Sat, 7 Apr 2001 11:43:20 +0400 Sender: val@nmr-v.ioc.ac.ru Message-ID: <3ACEC518.6EC8BE38@cacr.ioc.ac.ru> Date: Sat, 07 Apr 2001 11:43:20 +0400 From: Valentine Ananikov Reply-To: val@cacr.ioc.ac.ru Organization: IOC X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.13 i686) X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL_post Subject: Re: CCL:CCL = G98 userlist References: Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi, Your observation seems to be correct, some of Gaussian users are quick in asking and slow in reading manuals. However, dividing CCL into a series of topic specific sublists might not be a best solution. IMHO, not long ago a lot of technical questions concerning CHARM and Autodock have appeared (probably too much from Gaussian user's point of view). Should these be moved to sublists also? Of course CCL isn't directly supposed to be a universal theoretical chemistry software help desk. However, attempts to define discussion limits may not be the best way to keep the list active and interesting for a wide range of theoretically oriented chemists. It seems, it would be nice to mark ALL software specific questions, i.e. CHARM, Autodock, etc., to allow mail programs tuning for all of subscribers. best regards, Valentin. Rick Venable wrote: > > This topic has come up a couple of times before on CCL. > > I also feel the number of Gaussian specific questions and answers is too > high for what is supposed to be a GENERAL discussion list, and not a > Gaussian help desk. > > The main problems seem to be: > > (1) there isn't a good Gaussian mailing list already > (2) product support for Gaussian is not very good > > I value the breadth of contributions to CCL as well, but don't see how > that relates to whether or not there should be a specific Gaussian list. > > I happen to think a Gaussian specific list would be an excellent idea. > IMHO, that would be the proper place to discuss nuances such as memory > usage as a consequence of symmetry changes in G98. Attempts to create > such a list in the past, however, haven't been very successful, which is > why this topic has come up again. > > Fortunately, the message volume on CCL is reasonable, and it's easy to > delete messages with G98 in the Subject: line with most mail programs. > > > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > Rick Venable > FDA/CBER/OVRR Biophysics Lab > 1401 Rockville Pike HFM-419 > Rockville, MD 20852-1448 U.S.A. > (301) 496-1905 Rick_Venable@nih.gov > ALT email: rvenable@speakeasy.org > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > ==================================================================== , , , , Valentin P. Ananikov |\\\\ ////| /////| NMR Group | \\\|/// | ///// | ND Zelinsky Institute of Organic Chemistry | |~~~| | |~~~| | Leninsky Prospect 47 | |===| | |===| | Moscow, 119992 | | | | | | | Russia | | A | | | Z | | \ | | / | | / e-mail: val@cacr.ioc.ac.ru \|===|/ |===|/ http://nmr.ioc.ac.ru/Staff/AnanikovVP/ '---' '---' Fax +7 (095)1355328 Phone +7 (095)9383536 ==================================================================== From chemistry-request@server.ccl.net Sat Apr 7 12:55:49 2001 Received: from puck.reed.edu ([134.10.2.8]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f37GtmD18262 for ; Sat, 7 Apr 2001 12:55:48 -0400 Received: (qmail 2871 invoked from network); 7 Apr 2001 16:54:00 -0000 Received: from rosencrantz.reed.edu (134.10.2.31) by puck.reed.edu with SMTP; 7 Apr 2001 16:54:00 -0000 Message-id: <801994@rosencrantz.reed.edu> Date: 07 Apr 2001 09:55:36 PDT From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: CCL = G98 userlist To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f37GtnD18263 Valentine Ananikov wrote: it would be nice to mark ALL software specific questions, i.e. CHARM, Autodock, etc., to allow mail programs tuning for all of subscribers --- I strongly support this question, and I want to thank all of the people who have included program names in their subject line (when they have a question about a particular program). It has made it much easier for me to read my email. -Alan ==== Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202-8199 503-771-1112, ext. 7699 From chemistry-request@server.ccl.net Sat Apr 7 14:49:51 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f37InpD19898 for ; Sat, 7 Apr 2001 14:49:51 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id OAA08264; Sat, 7 Apr 2001 14:25:10 -0400 (EDT) Date: Sat, 7 Apr 2001 14:25:10 -0400 From: Rick Venable To: Valentine Ananikov cc: CCL_post Subject: Re: CCL:CCL = G98 userlist In-Reply-To: <3ACEC518.6EC8BE38@cacr.ioc.ac.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 7 Apr 2001, Valentine Ananikov wrote: > Your observation seems to be correct, some of Gaussian users > are quick in asking and slow in reading manuals. > > However, dividing CCL into a series of topic specific sublists > might not be a best solution. IMHO, not long ago a lot of technical > questions concerning CHARM and Autodock have appeared (probably too > much from Gaussian user's point of view). > Should these be moved to sublists also? There are independent mailing lists for programs like GAMESS, AMBER, CHARMM, etc. which deal with many more package specific questions than ever appear on CCL. If all these questions were also appearing on CCL, it would be a much busier list. Fortunately, Gaussian users are spared the details of tweaking input files, compiling for platform X, etc.; it would be nice if G98 users would return the favor. I don't think CCL should split up-- but I do lament the lack of a Gaussian mailing list, where a major percent of the Gaussian messages that appear on CCL would be more germane and appreciated. > Of course CCL isn't directly supposed to be a universal theoretical > chemistry software help desk. However, attempts to define discussion > limits may not be the best way to keep the list active and interesting > for a wide range of theoretically oriented chemists. I completely agree; the diversity of topics adds to the value of the Computational Chemistry List. Program specific minutiae, i.e. helpdesk questions, probably belong on another mailing list dedicated to that topic, however. In the case of Gaussian, I am somewhat surprised that the vendor hasn't shown more initiative, and established just such a mailing list. > It seems, it would be nice to mark ALL software specific questions, > i.e. CHARM, Autodock, etc., to allow mail programs tuning for all of > subscribers. The Subject: lines are up to the message submitter; most posts to CCL seem to have relevant ones which often include the program name, which is about all we can hope for. > Rick Venable wrote: > > This topic has come up a couple of times before on CCL. > > > > I also feel the number of Gaussian specific questions and answers is too > > high for what is supposed to be a GENERAL discussion list, and not a > > Gaussian help desk. > > > > The main problems seem to be: > > > > (1) there isn't a good Gaussian mailing list already > > (2) product support for Gaussian is not very good > > > > I value the breadth of contributions to CCL as well, but don't see how > > that relates to whether or not there should be a specific Gaussian list. > > > > I happen to think a Gaussian specific list would be an excellent idea. > > IMHO, that would be the proper place to discuss nuances such as memory > > usage as a consequence of symmetry changes in G98. Attempts to create > > such a list in the past, however, haven't been very successful, which is > > why this topic has come up again. > > > > Fortunately, the message volume on CCL is reasonable, and it's easy to > > delete messages with G98 in the Subject: line with most mail programs. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=