Re: CCL:I/O in Charmm

[Don Gregory <dgregory - at - msi.com>]

 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
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 Dr. Don Gregory (dgregory - at - 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