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#613 - 11/29/03 09:57 AM RTF'S & PARAMS for unusal compounds?
jb007 Offline
Forum Member

Registered: 09/30/03
Posts: 250
Loc: Florida State
It might be useful to have a link or forum for in-house developed parameters and residue topologies that are currently abscent in the official force-field version of CHARMM27.

Sincerely

Johan


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#614 - 12/01/03 04:31 PM Re: RTF'S & PARAMS for unusal compounds? [Re: jb007]
alex Offline

Forum Member

Registered: 10/04/03
Posts: 780

One of the problems with storage of "in house" parameters is that users
start to assume that they are well tested when this is often not true.
Untested parameters can often be very bad, leading to incorrect results.
My preference would be for individuals to announce that they have
parameters for a certain system and allow people to contact them
if they're interested.

I will also soon add additional topology and parameter information
for more small molecules on my web page. Based on the available
small model compounds, topology and parameter information
can often be generated by analogy. See the powerpoint file from
the Sanibel lecture on my web page for a good example.

alex
_________________________
School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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#615 - 12/02/03 02:30 AM Re: RTF'S & PARAMS for unusal compounds? [Re: alex]
jb007 Offline
Forum Member

Registered: 09/30/03
Posts: 250
Loc: Florida State
OK,
I have your sanibel-ppt, but unfortunately not the -98 paper directly available. Which charges are to be determined at the HF/6-31G* level of theory? (i.e. Mulliken, (R)ESP or other population analysis?

As for new/refined parameters, I've almost completed a set of higher valency metal ions which seems to perform well and follows a physically sound parameterization routine. Will send them to you when finally tested.

Johan

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#616 - 12/03/03 02:18 PM Re: RTF'S & PARAMS for unusal compounds? [Re: jb007]
alex Offline

Forum Member

Registered: 10/04/03
Posts: 780
The charges are based on the reproduction of interaction energies
and distances (with the applied scaling/offset) between the
model compound and individual waters at the HF/6-31G* level. This
procedure is described in all our parameter papers, including the supplemental
material from the JCC nucleic acid paper that is available on
my web page.

alex
_________________________
School of Pharmacy
University of Maryland
20 Penn Street
Baltimore, MD, 21201

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