Charles, all:
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?
The reason I ask is I am doing structural studies on peptides that have
N-methyl residues. At this point I do not want to explicitly create these
residue types. I would just like to increase the van der Waals radius of the
amide proton to approximate the size of a methyl group, keeping the van der
Waals interactions turned off for the covalent neighbor atoms of course.
As a specific example, if I have a peptide with N-methyl-leucine at resides 3
and 8, can I increase the van der Waals radius of the HN at position 3 and the
HN at position 8 selectively? Thanks for all of your help.
Keith Constantine
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]
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