Subject: Summary for I/O in Charmm

From: "Xiang(Simon) Wang" <[email-masked]>
Date: Thu, 14 Sep 2000 02:01:50 -0400 (EDT)

Dear CCLers:

Here is the summary for the answers to my original question of last week.
Sorry for my late summary. I worked it out by following Rick Venable's
suggestion: editing the existing RTF files. It works well with the
academic version of Charmm if the suitable RTF files are available. I
don't have QUANTA at hand, so I didn't try the the parameter chooser. 

Thanks a lot for all the answers.

X. WANG

---------------------------------------------------------------------
Original Question:

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?
----------------------------------------------------
Jerome Baudry, Ph.D. 

The best approach would be to go for ab initio
parametrization for your molecule. However, if you are using C25 or
higher, there should be a 'automated parameters calculator' in CHARMM that
can estimate missing parameters from the atom types. Now if insightII
produces atom types that are not in CHARMM's parameter file, CHARMM will
not be able to estimate the missing parameters. I suggest that you compare
all the atom types assigned by Insight to the atom types defined in
CHARMM's parameter file. If you find differences, you might want to change
the atom type in the psf to the corrresponding type in the parameter file.
----------------------------------------------------
Rick Venable 

If you want results of reasonable quality, you should create
the new molecule yourself, by editing a copy of an existing RTF file (one
for nucleic acids might be best) to create the PRPP molecule as a RESIdue
description using existing RESIdues as models to pick the correct atom
parameter types. 
----------------------------------------------------
Dr. Don Gregory 

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. 
---------------------------------------------------
Dr. Rebecca Rone 

If you have a copy of QUANTA that molecule should be no problem. Use
CHEMNOTE and its RTF generator. If it finds missing parameters, which it
shouldn't, it will recommend parameters from the parameter chooser. Be
certain first that all the atom types are properly assigned, i.e. mimic
the similar atom types as found in the DNA generator with approprate
changes. Then accept the parameters as suggested and write the PSF. Also
use the DNA generator to create a standard PSF and cross check the
parameters.