From bcnlma@hkpucc.polyu.edu.hk Mon Sep 18 00:17:16 1995 Received: from hkpv17.polyu.edu.hk for bcnlma@hkpucc.polyu.edu.hk by www.ccl.net (8.6.10/950822.1) id AAA10954; Mon, 18 Sep 1995 00:08:43 -0400 From: Received: from [158.132.30.106] ([158.132.30.106]) by hkpv17.polyu.edu.hk with SMTP; Mon, 18 Sep 1995 12:08:35 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 18 Sep 1995 12:09:27 +0800 To: CHEMISTRY@www.ccl.net Subject: G92 freq output Dear all, Is there anyone using g92 (not g94 or other versions) out there? I would like to use a PD program MOLWIN for PC to display vibration. However, the program only takes g92 frequency output file, not g94. So I have to figure out what is the difference between the 2 versions, but I do not have g92. Could someone who have g92 please contact me? Thanks in advance. yours sincerely, Ida N. L. Ma Dr. Ida N. L. Ma Assistant Professor, GH623, Dept. of Applied Biology and Chemical Technology Hong Kong Polytechnic University Hung Hom, Hong Kong Tel: 852-27665620 FAX: 852-23649932 From mrigank@imtech.ernet.in Mon Sep 18 05:02:20 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/950822.1) id EAA14481; Mon, 18 Sep 1995 04:49:57 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id OAA28222 for chemistry@www.ccl.net; Mon, 18 Sep 1995 14:20:35 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA23012; Mon, 18 Sep 95 10:09:34+050 Message-Id: <9509180509.AA23012@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Mon, 18 Sep 95 09:15:29 +0530 Date: Mon, 18 Sep 95 09:15:29 +0530 From: Mrigank To: chemistry@www.ccl.net Subject: RE: CCL:Cluster according to internal coordinates X-Vms-Mail-To: UUCP%"zhy@csb0.IPC.PKU.EDU.CN" ==>I've got from a simulated annealing process a group of conformations of a ==>penta-ptide with 3D coordinates, and want to cluster them according to ==>internal coordinates, i.e. value of Phi and Psi angle, but I haven't found ==>the relative function in SYBYL or QUANTA. Can anyone tell me where to find ==>suitable softwares ? ==> ==>BTW, I also want to get the standard of dividing Ramanchandra graph ==>(explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell ==>whether it fall into A,D,or D*? I have written a program which can find phi, psi, omega and chis from PDB or MoMoS format files and output in a cpmpact tabular or a GNUPLOT script that also markout the Ramachandran allowed regions. It is in Fortran. If interested i can send it . Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ FAX: +91 172 690585 / /Sector 39A, \/ Email: mrigank@imtech.ernet.in \ \Chandigarh 160 014 India. /\ mrigank@csimtech.ren.nic.in / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// Science does not have a country, But Scientist has one -L. Pastuer From mes@atlas.chemistry.uakron.edu Mon Sep 18 15:17:28 1995 Received: from dax.cc.uakron.edu for mes@atlas.chemistry.uakron.edu by www.ccl.net (8.6.10/950822.1) id PAA25209; Mon, 18 Sep 1995 15:11:19 -0400 Received: from atlas.chemistry.uakron.edu by dax.cc.uakron.edu (5.65/Ultrix4.3) id AA28400; Mon, 18 Sep 1995 15:13:40 -0400 Received: by chemistry.uakron.edu (4.1/SMI-4.1) id AA13342; Mon, 18 Sep 95 15:15:37 EDT Date: Mon, 18 Sep 1995 14:45:33 -0400 (EDT) From: Mary Ellen Scott Sender: Mary Ellen Scott Reply-To: Mary Ellen Scott Subject: VIDEO-Help To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hello, I am looking for a way to smooth out a video (VHS) which currently runs at 8 slides/sec and upgrade the picture quality to 20+frames/sec. The setup consists of a 486PC, OS2 system and the uncompresssed data can be converted to GIF, AVI and IMB Motion format. I have heard of MPEG but wonder if I need to go that way to achieve this enhancement. Any help would be appreciated. Thank you Mary Ellen From wriggers@london.ks.uiuc.edu Mon Sep 18 18:17:30 1995 Received: from london.ks.uiuc.edu for wriggers@london.ks.uiuc.edu by www.ccl.net (8.6.10/950822.1) id SAA28810; Mon, 18 Sep 1995 18:03:35 -0400 Received: from beograd.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.16/16.2) id AA108711815; Mon, 18 Sep 1995 17:03:35 -0500 From: Willy Wriggers Message-Id: <199509182203.AA108711815@london.ks.uiuc.edu> Received: by beograd.ks.uiuc.edu (NX5.67d/NX3.0X) id AA09563; Mon, 18 Sep 95 17:03:33 -0500 Date: Mon, 18 Sep 95 17:03:33 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@www.ccl.net Subject: protein domain movements: a new algorithm Dear all, I would like to present "Hingefind", a new algorithm to determine and visualize protein domain movements by comparing two structures. Below follows a short description of the method. It has been developed to investigate differences in crystal structures or computer simulated systems and I found it very useful for obtaining a coarse-grained description of the movements. Please access the Hingefind homepage for more info and an example of usage: ftp://lisboa.ks.uiuc.edu/pub/wriggers/hingefind/hingefind.html or download the whole distribution including documentation by anonymous ftp to lisboa.ks.uiuc.edu from the directory pub/wriggers/hingefind ! Cheers, Willy Wriggers _______________________________________________ wriggers@uiuc.edu (NeXT-mail OK) Willy R. Wriggers Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801, USA Telephone (217) 244-1612 Telefax (217) 244-6078 WorldWideWeb: http://www.ks.uiuc.edu/~wriggers/ _______________________________________________ "Hingefind" is an algorithm for the identification of domain movements and their characterization and visualization by hinge points and rotation axes. The method is implemented in X-PLOR 3.1 script language (Axel T. Brunger, 1992). The output psf and pdb files can be visualized with standard graphics packages. It compares two known structures (e.g. two different crystal structures of a protein or the results of molecular dynamics simulations) and partitions the protein with a prespecified resolution in preserved subdomains. It then determines effective hingeaxes which characterize the domain movements with respect to the reference domain. Both parts of the algorithm can be used alone, i.e. one can assign domains manually and let the algorithm determine the effective hingeregions between the domains, or one can use the algorithm to partition a protein into preserved subdomains. The method does not require any previous knowledge about functionally relevant domains or hinge motions, however a critical analysis of the results is recommended. The output files provide information about the accuracy of the found hinge-rotation. The variety of options and resolutions allow to find an optimal partitioning. The user can assess the validity of the proposed movement and test a variety of resolutions. From rosas@irisdav.chem.vt.edu Mon Sep 18 21:32:33 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/950822.1) id VAA00710; Mon, 18 Sep 1995 21:29:08 -0400 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id VAA20937; Mon, 18 Sep 1995 21:29:06 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9509182129.ZM20935@irisdav.chem.vt.edu> Date: Mon, 18 Sep 1995 21:29:02 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Summary: negative frequencies in MOPAC93 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi guys, Some time ago I posted a question about getting negative frequencies using the COSMO model in MOPAC93. If I delayed posting this summary, it was because I wanted to understand better the problem and give a useful summary. First of all, let me thank all those who responded: Dr. J. J. P. Stewart. Dr. Christopher J. Cramer Dr. Frederic A. van Catledge My original posting was: ******************************************************************************* It's me again :) I've got a weird problem with MOPAC 93. I trying to calculate free energies of solvation for several sets of conformers (no TS's involved). This involves calculating the frequencies and principal moments of inertia for each conformer, both in gas phase and in solution, to account for the entropic contribution to the free energy. I'm using FORCE for this, but every now and then I get a *negative* frequency even though there are no negative force constants in the force matrix. The problem is more frequent when I use FORCE and EPS=78.3, but it does appear for the gas phase calculations too. Usually there will appear one negative frequency with an absolute value less than 40 cm^-1 (sometimes two). FORCE found the gradients to be acceptable (<2) in all cases so no additional minimization was done by FORCE. According to the manual (regarding TS optimization) there is a way to get rid of spurious negative frequencies which is to run a DRC along the spurious mode. However, when I use Cerius2 to animate the negative frequency mode I see that it is quite complex. Basically all the atoms move, so it is not obvious to me how I can define a DRC along so many coordinates. BTW, the molecules I'm working on are either zwitterions or tetraalkylammonium cations (carnitine and choline). To make it brief my main questions are: 1) Is it possible to have a negative freq. and no negative force constant? 2) what meaning can be attached to a negative frequency (if any)? 3) Does it make sense to run FORCE and EPS=78.3 together? 4) Am I missing something really simple here? Thanks in advance. ******************************************************************************** Now, first of all, I have to make something clear. In the original posting, question number one was motivated by an error in reading MOPAC output: Basically I confused the FORCE MATRIX with the FORCE CONSTANT MATRIX. It was until later that I learned that the FORCE CONSTANT MATRIX is only printed when using the keyword LARGE. That's why I couldn't find any negative force constants in the matrix but that weird thing motivated some nice replies from some very cool people (names above). The answer to question number two is that those "negative" frequencies are actually *imaginary* frequencies, just printed out as negatives as a way to identify them. To question 3) the answer is: yes, it does make sense to use FORCE and EPS=78.3, *but* you can get into a lot of trouble. And the correction is not easy. Unfortunately I couldn't make it to the Chicago ACS meeting to hunt down Dr. Stewart and/or Dr. Andreas Klamt and learn anything about this problem. I guess the answer to question 4) is NO. I wasn't missing anything really simple. Now, some interesting facts I learned about MOPAC93 (courtesy Dr. Stewart): >In MOPAC, the six trivial >modes are explicitly calculated. This calculation is trivially simple >for the translations - for the `X' mode it is simply > >x 0 0 x 0 0 x 0 0 ... > >where x is 1/sqrt(n), with n being the number of atoms. The rotation >modes are more tricky - they involve the moments of inertia - but are >not too difficult. These six modes are projected out of the Hessian. So there is never ambiguity in assigning the trivial modes, BUT the six trivial modes are printed only if the keyword LARGE is used. To the suggestion that roundoff errors give rise to an artificial negative frequency or that the Hessian is computed by a single-difference approximation instead of a center-difference method. >In MOPAC double sided derivatives are used. If need be, quartic contamination >can also be removed. > >(...) the step-sizes involved are (...) typically 1/60 Angstrom. Also, when one wants to get rid of an imaginary frequency one could try running a reaction path calculation along the imaginary mode, but when a lot of the atoms move it is difficult to choose the right reaction coordinate. In this case it's better to use the keywords DRC and IRC=n, where n is the number of the mode one wants to get rid of. So, that's pretty much what I did: I started running series of reaction paths and DRC's on each molecule that had the problem and in a good number of cases that involved COSMO (I calculate approx. 80%) I got rid of the negative frequencies that were bothering me. WARNING: it was a VERY tedious procedure. I think that the main problem was that the geometries were not completely optimized, even though the energies varied very little. I was consistently getting the calculation stopped after the message "HEAT OF FORMATION IS ESSENTIALLY STATIONARY" which to me means that the potential energy surface is very flat, so there can be somewhat significant changes in the geometry without really affecting the energy. I think that the negative frequencies were a manifestation of that lack of geometric optimization (any other interpretations welcome). I don't know if COSMO requires extreme precision in the location of the minimum, but it could be (GNORM=0.01 didn't help because the message about the heat of formation kind of overrides the GNORM). BTW, the negative frequencies showed up usually in very soft potential modes, namely, carboxylate rotation, hydroxyl rotation and methyl rotation. I hope this summary made sense, I'm a little tired after teaching the whole day :( -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton -------------------------------------------------------------------------