From: saam (saam_at_ks.uiuc.edu)
Date: Tue Mar 11 2008 - 11:56:45 CDT

Dear Laura,

sorry for the late answer - I'm out of office these days.

1) The charmm charge module is very preliminary and does not really work
well yet. However I hope to be able to provide an updated version in a
couple of weeks. Some general info: The charge groups denote groups of atoms
whose chares is the force field must sum up to an integer value like -1, 0
or 1. A single chare group can have multiple hydration sites (which is not
represented yet in Paratool) and you adjust the charges of each hydration
separately, any residual charges must go to a 'dumpster' heavy atom, like an
aliphatic carbon. If you can't wait until I finish a better version of
Paratool , you have to do the charges yourself, following Mackerells
protocols (See Paratool user guide for weblinks).

2) The parameters that come from the projection of the hessian are not
symmetrized. When you assigned identical atom types to the chemically
equivalent bond or angles in your molecule you an use paratool to make the
parameters symmetric. When the parameters differ a lot, then this is a sign
that they are not equivalent. when you have two or more equivalent moieties
in your molecule then you should consider breaking up the molecule into
smaller model compounds.

Jan

2008/3/5 laura <stting0718_at_eyou.com>:

> Hi all,
>
> When I use the paratool to compute the missing Charmm parameters,
> something puzzle me.
>
>
> First is the Charmm charge. I transfer some "group" charges which is the
> existing Charmm molecule to the fragment model, and then, adjust the charges
> upon linking the group to form fragment model. I don't know whether this is
> reasonable.
>
> Second is about the results. I find there are some different parameters
> corresponding to the same type of bond or angle.
> For example, in the group of
> /H1
> C-C
> \H2
> the parameter of "C-C-H1" and "C-C-H2" is different. The same group in
> different positions of the whole molecule also corresponds to different
> parameter.
>
> How to control these parameters? Can I use the average of them?
> Thank you for any help!
>
> laura
>
>
>
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