From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Sun Aug 29 2004 - 21:01:52 CDT
Hi,
The documentation for psfgen, which is now a VMD extension module
rather than a standalone program distributed with NAMD, can be found
here:
http://www.ks.uiuc.edu/Research/namd/current/ug/node17.html
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.
Cheers,
Justin
On Sun, 29 Aug 2004 14:23:00 -0700 (PDT), Vani Krishna
<vakri2002_at_yahoo.com> 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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