From eugene@liposome.genebee.msu.su Sun Jun 28 10:41:02 1998 Received: from liposome.genebee.msu.su (eugene@liposome.genebee.msu.su [158.250.34.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA18058 Sun, 28 Jun 1998 10:41:00 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id SAA02364; Sun, 28 Jun 1998 18:44:45 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Sun, 28 Jun 1998 18:44:43 +0400 (MSD) To: "chemistry@www.ccl.net" Subject: advice on results ; X-PLOR parameter files for NaCl In-Reply-To: <35929E6D.6882B256@lauca.usach.cl> References: <35929E6D.6882B256@lauca.usach.cl> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13718.19966.983639.860570@liposome.genebee.msu.su> Dear CCLers, as part of my magistrate work I've made a number of MD simulations of solvated biopolymers. Though both results and the manner of presentation (beamer, movies, etc.) were well accepted locally, I am by no means certain that the results are not bogus. Can you advise? Polyelectrolyte part: I made fully charged polylysin (33mer and beyond, no hydrogens) with X-PLOR, and computed a few 10 ps worth of minimization and dynamics (Helmut Heller's EGO with FAMUSAMM electrostatics). As to be expected, in vacuo the equilibrium conformation is a string under tension. (Structure generated by Axel Br"unger's X-PLOR's standard peptide generation script heated spontaneously to 5-6 kK, after a few ps of minimization the system held the target 300 K stably, however). After adding chlorides as counterions, and a few ps of minimization dynamics the counterions are captured quantitatively, and initiate a rapid compactisation of the polylysin into a random coil, crosslinked by chloride ionic bridges. Each chloride acted as a coordination nucleus for 2-3 -NH3+ groups. The equilibrium conformation did not relaxate noticeably after having been subjected to solvatation (TIPS3P; Helmut Grubm"uller's Solvate 1.0) within 20-30 ps. Solvated initial conformation in the beginning showed similiar dynamics, however vastly inhibited though charge shielding and viscous drag. (Due to lack of time and system size the results are very preliminary). To this part, I have the following questions. I used the following parameter files for NaCl, which the original author deemed unvalidated, and possibly unreliable. parameter: NONBonded NAI 0.026 1.470 0.026 1.470 NONBonded CLI 0.26 1.835 0.26 1.835 topology: MASS NAI 22.99000 MASS CLI 35.45000 RESIdue INA GROUp ATOM NA TYPE=NAI CHARge= 1.000 END END RESIdue ICL GROUp ATOM CL TYPE=CLI CHARge= -1.000 END END However, another source suggested the following parameters for Cl: NONBONDED LC 0.0430 3.3676 0.0430 3.3676 (topo the same, hence omitted). Which parameters are correct? (the difference in the values seem to indicate there is either no consensus, or one/both of these sets is/are bogus). Are there any canonical, validated ones out there? Is there a depository for param/topo files somewhere to be found? Since we are at that, how _does_ one derive parameter files? Unless this is a real black art, I'd be thankful for any references. (Having to rely on opaque semiempirical force fields is bad enough, but feeding them with opaque ad hoc parameters of dubitable lineage is even worse). [ second part on questions on phospholipid modelling now omitted for brevity ] Thanks! Regards, Eugene Leitl From cdac.ernet.in!gadre@parcom.ernet.in Sat Jun 27 09:05:10 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA13210 Sat, 27 Jun 1998 09:03:01 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id SAA15590 for ; Sat, 27 Jun 1998 18:43:09 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA08582; Sat, 27 Jun 1998 18:30:04 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA00507; Sat Jun 27 18:28:08 1998 (GMT + 0530) Date: Sat Jun 27 18:28:08 1998 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9806271258.AA00507@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Contacts of phenyl and methyl groups Dear Sirs and Madams : Pardon me for this query. Maybe the answer is too well-known. Could you give me references to searches done using crystallographic databases of the following. 1. Contacts of a phenyl ring with a nearby acidic hydrogen hanging above the ring. 2. Contacts of an acidic H atom with a methyl group. Thanks a lot!.....................................Shridhar Gadre From richard@tc.cornell.edu Sun Jun 28 13:55:21 1998 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA18858 Sun, 28 Jun 1998 13:55:21 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id NAA18936; Sun, 28 Jun 1998 13:55:20 -0400 Sender: richard@tc.cornell.edu Message-ID: <35968387.2781@tc.cornell.edu> Date: Sun, 28 Jun 1998 13:55:19 -0400 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Yongxing Liu CC: chemistry@www.ccl.net Subject: Re: CCL:Programs that can perform MD only in torsional space References: <199806280100.VAA17762@mail.wesleyan.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > I want to know if there exists one program that can perform Molecular > Dynamics Simulation only in torsional space. I think Harold Scheraga's group published such an algorithm at least 6 or 8 years ago. (sorry I don't have the ref anymore). I recall the theory reminded me of automatic Talyor series expansion methods (Y.F. Chang, early 80's). Richard Cornell Theory Center From m.dooley@mailbox.uq.edu.au Sun Jun 28 19:04:20 1998 Received: from bunyip.cc.uq.edu.au (root@bunyip.cc.uq.edu.au [130.102.2.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA19592 Sun, 28 Jun 1998 19:04:18 -0400 (EDT) Received: from peta.ddd.uq.oz.au (peta.ddd.uq.edu.au [130.102.118.65]) by bunyip.cc.uq.edu.au (8.8.8/8.8.8) with SMTP id JAA18782; Mon, 29 Jun 1998 09:04:18 +1000 (GMT+1000) Received: from extreme.ddd.uq.oz.au by peta.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) id JAA07045; Mon, 29 Jun 1998 09:03:24 -1000 Received: from chico.ddd.uq.oz.au by extreme.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI) id JAA05721; Mon, 29 Jun 1998 09:03:22 -1000 Received: from mailbox.uq.edu.au by chico.ddd.uq.oz.au via ESMTP (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) id JAA02975; Mon, 29 Jun 1998 09:03:20 -1000 Sender: dooley@mailbox.uq.edu.au Message-ID: <3597E4F7.45A7FE4B@mailbox.uq.edu.au> Date: Mon, 29 Jun 1998 09:03:20 -1000 From: Michael Dooley X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: yliu@wesleyan.edu, chemistry@www.ccl.net Subject: Re: CCL:Programs that can perform MD only in torsional space References: <199806280100.VAA17762@mail.wesleyan.edu> <35968387.2781@tc.cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Richard Gillilan wrote: > > I want to know if there exists one program that can perform Molecular > > Dynamics Simulation only in torsional space. > > I think Harold Scheraga's group published such an algorithm > at least 6 or 8 years ago. (sorry I don't have the ref anymore). > I recall the theory reminded me of automatic Talyor series expansion methods > (Y.F. Chang, early 80's). The program is available from QCPE (qcp664). Be careful though, we never got it to compile because it requires some libraries we didn't have (and they cost $$). Cheers Michael -- Michael Dooley PhD Centre for Drug Design and Development The University of Queensland Brisbane Qld 4072 Australia m.dooley@mailbox.uq.edu.au