Re: vmd-l: Protonated GLU/ASP in PSF generation

From: Justin Gullingsrud (
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
<> wrote:
> Hello
> 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
> Thanks
> Vani
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