From chpajt@bath.ac.uk Sun Jun 30 03:57:22 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.5/950822.1) id DAA14518; Sun, 30 Jun 1996 03:24:46 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Sun, 30 Jun 1996 08:24:35 +0100 Date: Sun, 30 Jun 1996 08:24:30 +0100 (BST) From: A J Turner To: chpajt@bath.ac.uk cc: chemistry@www.ccl.net Subject: Re: MM IR spectrum of solvated system @ 80 C In-Reply-To: <9606291726.AA09966@auriga.rose.brandeis.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I need to generate the ir spectrum for a TIP3P solvated system at 80 C. I.E. a single point hessian at 0 K will not do the job! Does any one know how to do this or have any good references for it as a technique, using dynamics (Verlet in Charmm if poss). I am wondering if it is possible to generate a mean hessian matrix by taking the gradient vectors from a number of points in an equilibrium trajectory and use these for either F.T. or, say, Powell hessian update to achieve a representative set of frequencies. I also promise to summarise to ESP stuff in the next few days, as I will be local to the machine with all the stuff on it. Thanks for any ideas Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. | | ------------------------------------------------------------------- From raman@bioc01.uthscsa.edu Sun Jun 30 18:57:29 1996 Received: from elzip.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.7.5/950822.1) id SAA16946; Sun, 30 Jun 1996 18:31:43 -0400 (EDT) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01I6HFEU2YUC0095YU@uthscsa.edu>; Sat, 29 Jun 1996 14:14:19 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA12566; Sat, 29 Jun 1996 14:13:23 -0500 (CDT) Date: Sat, 29 Jun 1996 14:13:19 -0500 (CDT) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: CCL:Protein Interaction & molecular dynamics In-reply-to: <9606290806.AA20960@risc1.lrm.fi.cnr.it> To: antonio@risc1.lrm.fi.cnr.it (Antonio Rosato) Cc: chemistry@www.ccl.net Message-id: <9606291913.AA12566@bioc01.uthscsa.edu> X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Antonio: > I would like to know whether programs exist (either free or > commercial) which perform molecular dynamics with the aim > of simulating protein-protein recognition. My favorite program for doing protein docking and studying protein-protein interaction is ICM from Dr. Ruben Abagyan. You can contact him at: abagyan@earth.med.nyu.edu It is a truly exceptional program for structural studies. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ "The real problem in speech is not precise language. _/ _/ The problem is clear language." --Richard Feynman _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/