From chemistry-request@server.ccl.net Sun Sep 3 20:00:29 2000 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA25566 for ; Sun, 3 Sep 2000 20:00:28 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id QAA04558 for ; Sun, 3 Sep 2000 16:55:58 -0700 (PDT) Received: from unknown(146.202.11.79) by mailhost.msi.com via smap (V2.0) id xma004556; Sun, 3 Sep 00 16:55:57 -0700 Message-Id: <4.3.1.2.20000903162527.00b32d20@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 4.3.1 Date: Sun, 03 Sep 2000 16:47:59 -0700 To: CHEMISTRY@ccl.net From: Don Gregory Subject: Re: CCL:I/O in Charmm In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi all, Really, there are two separate issues here; (a) using InsightII to create CHARMm input files, and (b) what to do when a chosen force-field is missing parameters. The easy one first: Indeed, InsightII can write CHARMm PSF and RTF files. Whenever your research leads you to modify the (more or less) 'standard' molecule/residue types that are provided in the RTF files that come with InsightII, we heartily recommend you use the PSF creation capabilities of InsightII to make the 'whole-system' unique molecular topology description that CHARMm needs, i.e. the PSF file. That is what this capability is intended for. However, even given this, missing parameters are still a possibility since creating a topology is trivial comapred to developing a well optimized force-field that will cover all the esoteric molecular types you might encounter in your on-going research. MSI provides numerous force-fields, and are committed to extending our force-field coverage as we go forward. However if the force-field you are using (not specified in the original email) is missing parameters, we'd suggest CFF if that is not being used already. If CFF also is missing the parameters, then we're in the same boat as we've seen in dozens of emails here on the CCL, i.e. you can research the literature to see if someone has developed parameters *for that specific force-field* (if for another force-field, then you have to make the decision as to whether to accept the *approximation* that those parameters will be reasonably transferrable into the force-field you would like to use), or you can ask your collegues on CCL (remembering to specify the force-field you are using, and a complete description of the atoms (atom-types) involved [*not* as I've seen numerous time "has anyone developed parameters for X?"; not saying for which force-field and simply *assuming* transferrability is acceptable), or contact MSI to see if we have developed these parameters, ir ..... well, resort to a force-field optimization project yourself! In fact, it is 'fair' (?) to provide numbers from any of the sources mentioned above, but what is *really* crucial, is to note the original force-field used, and any added/modified parameters to that force-field, when publishing your results. This is a step that I think is missing all too often in molecular mechanics studies I've seen in the literature. There are additional comments to be found at MSI's scientific support FAQ site, under the heading of "ForceFields", http://www.msi.com/support/FAQ.html Hope this helps; sorry for such a long email. DG At 06:37 PM 9/3/00 -0400, Xiang(Simon) Wang wrote: >Dear CCLers: > >Can someone help me on how to read small molecule structure in Charmm? >For example, phosphoribosyldiphosphate (PRPP), which can not be found in >top_all22_model.inp file. I could get the PSF file from InsightII. But >when running, Charmm gave the warning of lacking of parameters. Can >someone help me out of it? > >Thanks a lot, > >X. Wang > > >-= 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. Don Gregory (dgregory@msi.com) CHARMm Product Marketing Manager Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (858) 799-5331 http://www.msi.com Mobile Ph.: (619) 200-3613