From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Sun Aug 29 2004 - 21:01:52 CDT
The documentation for psfgen, which is now a VMD extension module
rather than a standalone program distributed with NAMD, can be found
The syntax for the patch command is
patch <pres> <segid>:<resid> ...
where segid is the name of the segment containing the residue you want
to modify. Thus, for example,
patch ASPP PRO:57
would protonate Asp57 of segment PRO.
On Sun, 29 Aug 2004 14:23:00 -0700 (PDT), Vani Krishna
> How do i give the information in PSF gen script that i
> want residue XXX and resid YYY to be a protonated
> residue? Iam unsure of how to use the residue patches
> fro residues like ASP (ASPP)?
> Any help will be greatly appreciated
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-- The spirit of Plato dies hard. We have been unable to escape the philosophical tradition that what we can see and measure in the world is merely the superficial and imperfect representation of an underlying reality. -- S.J. Gould, "The Mismeasure of Man"
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