From chemistry-request@server.ccl.net Sun May 16 23:57:11 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA29285 for ; Sun, 16 May 1999 23:57:11 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id XAA03472; Sun, 16 May 1999 23:52:51 -0400 (EDT) Date: Sun, 16 May 1999 23:52:50 -0400 (EDT) From: Jan Labanowski To: Christoph Maerker cc: chemistry@ccl.net, Jan Labanowski Subject: Re: apache server - htpasswd missing In-Reply-To: <199905151641.SAA04271@chris2.u-strasbg.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 15 May 1999, Christoph Maerker wrote: > Universite Louis Pasteur > Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE > Phone: +33/3-88-41-53-19 > Fax: +33/3-88-60-63-83 > X-Mailer: ELM [version 2.4ME+ PL37 (25)] > MIME-Version: 1.0 > Content-Type: text/plain; charset=US-ASCII > Content-Transfer-Encoding: 7bit > Content-Length: 181 > > Hi all, > > I've got an apache www server. I want to passwd-protect some dirs, > but the htpasswd command is missing. How can one create this command, please ? > > Best regards, > Christoph > Dear Christoph, The passwords for the .htaccess mechanism of controlling access to the directories are created by the same mechanism as for UNIX login, i.e, /etc/passwd If you do not have perl installed, you can just change your password temporarily on the UNIX box by using passwd command and then copy the password to the Web password file. But this is cumbersome. The UNIX password is created with the crypt routine. It consists of "seed" (first two characters of password) and the encrypted password. The seed is composed of letters, digits, and few other printable characters, and is a parameter (2nd) to the crypt UNIX routine together with the "open text password" (1st). The crypt routine returns seed and enctrypted password as a string. encrypted_password = crypt(open_password, seed); perl has a crypt function, so you could generate password by just typing this at UNIX prompt: perl print STDOUT crypt("my_open_password", "7x"), "\n"; ^D 7xUC7SQVQeS.U Where, my_open_password, is the password which you want to encrypt, 7x is a seed (or salt, as people call it), ^D stands for CTRL/D, i.e,. end of transmission ASCII character, i.e, UNIX end of input. The encrypted password will be 7xUC7SQVQeS.U in this case. While it is so easy to generate encrypted password, there is no known way to go from encrypted password to the unencrypted password beside doing brute force checks and comparison with a dictionary (or guessted password). Note that a person who knows encrypted password, knows also the seed. Warning: you should not use the same passwords for Web and for UNIX log in. UNIX will throw you out after few bad tries and will make you wait. The Web usually will not punish password cracking, and it is much easier to crack the Web password (essentially unlimitted number of tries within short period of time) than the UNIX password which punishes the wrong entry with a wait period. Now, assuming that you want to use a script to make an encrypted password, this will do it for you (save it, and give it x permissions, and put the right location of perl on the first line). It will also generate a random seed for you. ----------------- cut and save as make_passwd.pl ------------------ #!/usr/local/bin/perl # generate encrypted password using the argument given # Usage: make_passwd.pl password @chars = ('a'..'z', 'A'..'Z', '0'..'9', '.', '/'); $n = $#chars + 1; $n2 = $n*$n; $seed = (time - $pid + (-s '/var/log/messages') + 1346235) % $n2; $seed1 = int($seed / $n); $seed2 = int($seed % $n); $salt = $chars[$seed1] . $chars[$seed2]; if($#ARGV == 0) { $encpasswd = crypt($ARGV[0], $salt); } else { die "Usage: make_passwd.pl plain_text_pass\n"; } print STDOUT "Encrypted Password = |$encpasswd|\n"; ------------------ cut -------------- Example: make_passwd.pl 'My*Secret' Encrypted Password = |4v2FWV9S1AbyQ| Your open password was My*Secret (the example does not imply that this is the good password, it is actually one of the worst), and the encrypted password in this case was 4v2FWV9S1AbyQ (note, the 4v is the seed which program automatically created). Now, how to protect your directory under Apache? Assuming that the directories which you want to protect are allowed in the Apache httpd.conf file to have password protection (e.g., if your directories are under, say, /web/private as in example below: AllowOverride Limit AuthConfig Options AuthType Basic AuthName private-web Options ExecCGI you can protected them easily. In the directory, which you want to protect, you place the file: .htaccess This file allows you to override some options from your httpd.conf file. For example: --------------- cut ----------- AuthUserFile /etc/httpd/auth/htpasswd AuthGroupFile /etc/httpd/auth/htgroup AuthName "For close friends only" AuthType Basic require group myfriends ------------ cut --------- In the directory /etc/httpd/auth (or whatever you choose, but do not put it in your Web tree), you create files htpasswd and htgroup (or whatever names you want to give them). For example: --------- cut: htpasswd ------------ jim:.lh4hjkcz.lFxE joe:/wuDR9867DJNE pipi:d/87ghkRTmIQ -----------cut ------------------- -------- cut: htgroup ------------- myfriends:jim joe pipi --------- cut ----------- The stuff which follows colon in httpasswd is encrypted password created as described above. All files should be world readable. Have fun, and remember that if you want to really protect stuff which you serve over the Web, you need to use SSL protocol -- this simple password protection does not encrypt communications, i.e., the passwords and the content. But SSL and ssleay is another story, and cannot be described in a one-pager, it is slightly more complicated. Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Mon May 17 00:54:27 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA29798 for ; Mon, 17 May 1999 00:54:26 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id AAA04146; Mon, 17 May 1999 00:48:29 -0400 (EDT) Date: Mon, 17 May 1999 00:48:29 -0400 (EDT) From: Jan Labanowski To: Eric German cc: chemistry@ccl.net, Jan Labanowski Subject: ab initio basis sets In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL, can you give better answers than my naive explanations? I did not look at these issues of ages... Jan jkl@ccl.net Actually, your question is a good one for CCL, and you may want to send it there to get opinions from experts in basis sets (I am not an expert in any way). Also, I did not look at the papers... My short comment: 1) Getting the good basis set is a a black art. While there is a systematic ways to get good basis sets (e.g., Dunning's correlation consistent basis sets), these sets are usually much larger than "ad hoc" (sorry, should be "intuitively optimized") basis sets. 2) You contract the inner s/p orbitals for at least 2 reasons: a) they usually do not change much on bonding, since most changes are in the valence orbitals b) to prevent core collapse -- the inner orbitals have VERY low energy (very large negative), and if uncontracted, the SCF optimization would first try to optimize coefficients for these orbitals rather than valence ones. 1% change in core orbital coefficient can make larger energy change for heavier elements than 50% change in a valence orbital coefficient. So, it is safer to keep them contracted, since they are not optimial for molecular calculations as they are derived from atomic calculations. 3) How contractions are done... Again, it is an art... But in short, people can get accurate numeric Hartree-Fock atomic calculations and fit exponents and coefficients for gaussian expansion of numeric AOs. They can also vary exponents and coefficients for atomic calculations since these computations are computationally feasible. But when we go to molecules, we have to limit the basis set size, or it would not finish in our lifetime, and also, there are many molecules to try. So what people do, they try to pull together some basis functions (contract them) and redo the calculations using either atomic (most often) or simple/representative/ molecular calculations to see how much energy they loose on going from uncontracted -> contracted. If energy change is small, contraction scheme is acceptable, if energy change is big, they try to come with different contraction scheme. And the big/small is in the eye of the beholder, and also depends on particular varian of ab initio (HF vs plethora of MCSCF and correlated methods) so often there are different contractions schemes for the same set of primitive gaussians. Note also that even for, say 20 primitive gaussians, you have a lot of possible contractions (factorials are involved), and rarely all possible contraction schemes are tried to see which one gives the lowest energy. So in many cases, there is a chance to design some new contraction scheme for the old set of primitive (i.e., uncontracted) gaussians. On Sun, 16 May 1999, Eric German wrote: > > > > Dear Dr. Lobanowski, > I have not any experience in using of ab initio basis sets but I > would like calculate complexes involving atoms of Pd. > I would greatly appreciate if you could clear me the following > problems with the contracted basis. Hay and Wadt have published > (JCP,1985) the basis (3s3p4d) for Pd (see 1-st and 2-nd columns of > table below. > > (3s3p4d) [2s2p2d] [2s1p1d] > --------- > alpha_i C_i C_i C_i > > 5s-orbitals > 1 1 1 > .4496 -.3594574 -1.166 -.3594574 > .1496 .5467561 1.6763 .5467561 > 2 2 > .0436 .7414499 1.00 .7414499 > 5p-orbitals > 2-4 3-5 3-5 > .7368 .03491 .0763285 .03491 > .0899 .4454769 .974006 .4454769 > 6-8 > .0262 .6611266 1.00 .6611266 > 4d-orbitals > 5-9 9-13 6-10 > 6.091 .0447293 .0511957 .0447293 > 1.719 .4425814 .5506564 .4425814 > .6056 .5051035 .578125 .5051035 > 14-18 > .1883 .2450132 1.00 .2450132 > > 9 basis funct., 18 basis funct., 10 basis funct., > 32 Gaussians 32 Gaussians 32 Gaussians > > 2) There is the standard basis LANL1DZ in Gaussian94 for Pd. It is the > contracted basis (3s3p4d)/[2s2p2q] (column 3 above). We see that this > contraction increases the number of basis functions and increases CPU > time. So, my question is: why this contraction is done and what is idea > to do the contraction of the first and the second Gaussians but not, for > example, of the first and the third for 5s-orbitals, and so for 5p > Gaussians? Are the corresponding coefficients in column 3 obtained by the > optimization procedure? > 3) In Column 4 is given the contracted basis (3s3p4d)/[2s1p1d] > of Akinaga et al (J.Chem.Phys,109 (1988) 11010 ). We can see that the > coefficients of this basis is the same as of the uncontracted basis > (3s3p4d). How do you think, what could be idea of this contraction? > Many thanks in advance > > Best wishes > Sicerely > E.D. German > > Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Mon May 17 03:32:32 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA30951 for ; Mon, 17 May 1999 03:32:32 -0400 Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id AAA20082; Mon, 17 May 1999 00:28:09 -0700 (PDT) Received: from localhost by redox.scripps.edu (8.9.1/TSRI-2.8) with SMTP id AAA27464; Mon, 17 May 1999 00:28:07 -0700 (PDT) Date: Mon, 17 May 1999 00:28:07 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Christoph Maerker cc: ccl Subject: Re: CCL:apache server - htpasswd missing In-Reply-To: <199905151641.SAA04271@chris2.u-strasbg.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 15 May 1999, Christoph Maerker wrote: > Hi all, > > I've got an apache www server. I want to passwd-protect some dirs, > but the htpasswd command is missing. How can one create this command, please ? > > Best regards, > Christoph Hi Christoph, Jan gave you an script that will do the work of the program you ask for, alternatively you could get one of the many pre-compiled distributions of Apache (www.apache.org), which will contain the missing program. Or, if your OS does not have a binary distribution, just get the source code and compile it. BTW, there are several free replacements in C code for the same program. Good luck. -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Mon May 17 04:23:59 1999 Received: from mozart.us.es (mozart.us.es [150.214.145.57]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA31498 for ; Mon, 17 May 1999 04:19:52 -0400 Received: by mozart.us.es (1.38.193.4/16.2) id AA00560; Mon, 17 May 1999 10:06:21 +0100 Date: Mon, 17 May 1999 10:06:20 +0100 (WETDST) From: Jose Manuel Martinez Fernandez To: chemistry@ccl.net Subject: nucleotide structures using amber? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I'm trying to simulate single stranded DNA using DL_POLY package. Force Field I'm using is AMBER (JACS'95, vol. 117, 5179-5197) In order to check if I correctly implemented the FF, I would appreciate if anyone could send me optimized structures obtained with other programs and their corresponding energies using amber95. Just two or three linked nucleotides I think is enough to test all the terms. thanks in advance, josema __________________________________________________________ _ _ _ Jose Manuel Martinez Fernandez, Ph.D. _ _ Dept. de Quimica Fisica, Universidad de Sevilla _ _ Facultad de Quimica, SEVILLA 41012, SPAIN _ _ e-mail: jmmartin@cica.es _ _ josema@mozart.us.es _ __________________________________________________________ From chemistry-request@server.ccl.net Mon May 17 04:58:57 1999 Received: from iris.chem.cuhk.edu.hk (iris.chem.cuhk.edu.hk [137.189.38.205]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA31792 for ; Mon, 17 May 1999 04:58:56 -0400 Received: (from carol@localhost) by iris.chem.cuhk.edu.hk (8.9.1/8.9.1) id BAA14998; Mon, 17 May 1999 01:32:52 -0700 (PDT) Date: Mon, 17 May 1999 01:32:52 -0700 (PDT) From: "Carol Y.Y. Au" To: chemistry@server.ccl.net Subject: Fermi Contact Contribution. Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1984092467-823873151-926575103=:9448" Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1984092467-823873151-926575103=:9448 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Dear CCLers, I have used the keyword FIELD to calculate the Fermi Contact term of water: #P UHF/3-21G Field=F(2)30 and I got the following results: Isotropic Fermi contact couplings: 1 1 H 0.001198 2 O -0.433339 3 H 0.001198 Firstly, I would like to know what is the units of the above numbers since it is not stated in the G98 manual? According to J.A.Pople's paper, J. Chem. Phys.1968, 49, 2960-2964, 2965-2970, Jab = (h/2*PI)(8*PI*B/3)(8*PI*B/3)[(Ra*Rb)/lamda] *Summation Puv(u) where B is the Bohr magneton, Ra and Rb are the magnetogyric ratio for nuclei a and b respectively, lamda is the perturbation parameter, Puv(u) is the uvth element of the spin density matrix evaluated at nucleus b, delta(r) is the Dirac delta function at the position of the nucleus a, phi u and phi v are atomic orbitals. Finally, I would like to ask that the above numbers that I obtained in the output file refers to which terms of the above equation? Thank you for your kind attention. Yours sincerely, Carol Au Nuclear Magnetic Resonance Group Dept. of Chem. CUHK E-mail :carol@iris.chem.cuhk.edu.hk Phone :(852) 2609 6167 Fax :(852) 2603 5057 ---1984092467-823873151-926575103=:9448-- From chemistry-request@server.ccl.net Mon May 17 06:35:34 1999 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA32708 for ; Mon, 17 May 1999 06:35:31 -0400 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (PP); Mon, 17 May 1999 11:31:08 +0100 From: uccatvm Message-Id: <16578.199905171031@socrates-a.ucl.ac.uk> Subject: Re: How to calculate BSSE of a 3-molecule system? To: chemistry@server.ccl.net (CCL) Date: Mon, 17 May 1999 11:31:07 +0100 (BST) Cc: T.vanMourik@ucl.ac.uk (Tanja van Mourik) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi Yubo, To compute the interaction energy of a trimer ABC, the energy of each fragment has to be calculated in the trimer basis set {ABC}. In the Gaussian program package, one can simply achieve that by using the trimer basis set to compute the energy of A while "massaging" the nuclear charge of all atoms of molecules B and C to zero (and the same for the energies of B and C). When you fully optimize the geometry of your system ABC, then you also have to take into account the monomer deformation energies Udef, which is the energy required to bring a molecule X from its equilibrium geometry (re) to the geometry it has in the complex (rx). The equation for computing the counterpoise-corrected interaction energy then becomes (in curly brackets the basis set used): De(CP) = E(ABC){ABC} - E(A){ABC} - E(B){ABC} - E(C){ABC} + + Udef(A) + Udef(B) + Udef(C) With Udef(X) = E(X){X}(rx) - E(X){X}(re) You might also want to look at a recent discussion on CCL on BSSE in calc. of activation energies. Kalju Kahn summarized the discussion on the list. Hope this helps, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)171-504-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Mon May 17 11:40:18 1999 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03205 for ; Mon, 17 May 1999 11:40:12 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.8.8/jtpda-5.3) with ESMTP id RAA28868 ; Mon, 17 May 1999 17:35:49 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.8.7/8.8.7) id RAA20323; Mon, 17 May 1999 17:35:04 +0200 Date: Mon, 17 May 1999 17:35:04 +0200 Message-Id: <199905171535.RAA20323@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: josema@us.es CC: chemistry@ccl.net In-reply-to: (message from Jose Manuel Martinez Fernandez on Mon, 17 May 1999 10:06:20 +0100 (WETDST)) Subject: Re: CCL:nucleotide structures using amber? References: > In order to check if I correctly implemented the FF, > I would appreciate if anyone could send me optimized > structures obtained with other programs and their > corresponding energies using amber95. Just two or three > linked nucleotides I think is enough to test all the > terms. It would be even better if someone could provide a publicly accessible set of test cases. Test cases should be small systems in order to simplify analysis, and provide as much information about individual energy terms as possible. Ideally such a set of test cases should be available for all the popular force fields. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 17 13:51:35 1999 Received: from mailc.surrey.ac.uk (mailc.surrey.ac.uk [131.227.100.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA04443 for ; Mon, 17 May 1999 13:51:35 -0400 Received: from ces1mb (actually host pcmb.mis.surrey.ac.uk) by mailc.surrey.ac.uk with SMTP (PP); Mon, 17 May 1999 18:47:11 +0100 Message-Id: <3.0.6.32.19990517184405.00814410@pop.surrey.ac.uk> X-Sender: ces1mb@pop.surrey.ac.uk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 17 May 1999 18:44:05 +0100 To: chemistry@server.ccl.net From: "Dr. M. Biggs" Subject: rule based determination of spectra Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi! I am starting to look at the calculation of various spectra (FTIR, RAMAN, NMR, X-ray, electron, neutron, EELS) based upon a known molecular structure. I would greatly appreciate some information on key reviews/texts which talk about how to calculate spectra for a known molecular structure using *rule-based approaches* (i.e. not QM calcs as I want to look at many structures). I am not sure such rule-based approaches exist but I suspect they do and I have heard that atleast for FTIR they do as they are available in commercial softwares. I will summarize if you like. Many Thanks in advance. Regards, Mark e-mail: m.biggs@surrey.ac.uk