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Article ID: 558 - Last Modified: May 13, 2011

I would like to use some of these keywords but the explanation in the Glide manual is not clear to me. Could you please provide me with some more information?

ASLSTRINGS list
GLIDERECEPTORSCALECHARGES list
GLIDERECEPTORSCALERADII list

All three of these are comma-separated lists. There must be the same number of list members in each, because these keywords indicate what groups of atoms get what vdw and charge scaling factors.

In the Glide Grid Generation GUI, the per-atom scaling table (on the Receptor tab) is organized such that each line specifies:
1) an ASL expression for the group of atoms,
2) the vdW scaling factor for those atoms,
3) the charge scaling factor for those atoms.

In the jobname.in file, this data is essentially changed into keywords for the three columns.

Example keywords are:

ASLSTRINGS "(chain.name A and res.num 99)", "(chain.name A and res.num 57)"
GLIDERECEPTORSCALERADII 0.900000, 0.800000
GLIDERECEPTORSCALECHARGES 0.900000, 0.800000

Please note that atoms for which per-atom scaling factors aren't specified are assigned the global values. The global vdW radius scaling for non-polar receptor atoms can be adjusted in the middle section of the Receptor tab.

Keywords: GLIDE receptor scale, keywords, lists, ASL string , values

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