Hi Charles,
Thanks a lot - this works fine.
I used:
parameter
nonbond (resid X and name HN) 0.0498 4.0000 0.0498 4.000
end
If I am correct, setting sigma to 4.000 should correspond to a radius of ~1.30
angstroms, which is close enough for this application.
Best regards,
Keith
Keith L. Constantine, Ph. D.
Sr. Research Investigator II
Mechanistic Biochemistry
Bristol Myers Squibb Research and Development
P.O. Box 4000
Princeton, NJ 08543-4000
Tel: (609)-252-6926
Fax: (609)-252-6012
e-mail: [email protected]
>-----Original Message-----
>From: Charles Schwieters [mailto:[email protected]]
>Sent: Friday, October 18, 2013 10:24 AM
>To: Constantine, Keith
>Cc: [email protected]; Charles Schwieters; Mueller, Luciano
>Subject: Re: changing van der Waals radius without modifying an atom
>type
>
>
>Hello Keith--
>
>>
>> Do you know how to increase the van der Waals radius of a specific
>atom in a
>> molecule without creating a new atom type or changing the radius in
>the
>> parameter file?
>
>Yes- using atom-based parameters.
> (e.g. http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node56.html)
>
>From the python interface, please try this:
>
>xplor.command("""
>parameter
> nonbond (resid X and name HN) 0.0498 1.4254 0.0498 1.4254
>end""")
>
>where you must specify X and change VDW parameters as you wish.
>
>best regards--
>Charles
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