VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Mon Aug 02 2004 - 16:06:43 CDT

Hi Alexis,

If you're using Charmm topology files, patch residues exist that let
you change residues from one protonation state to another. It's up to
you to decide which residues to modify however; you'll need to do a
pKa calculation or the equivalent to determine what protonation state
the residue should be in. Alternatively, you can use the constant-pH
feature in Amber8 and let the program determine protonation for you,
on the fly. This calculation would probably not be as accurate as
what a program such as Delphi or APBS would give, but would have the
advantage of telling you how protonation states were related to the
backbone conformation of the protein.

Cheers,
Justin

On Mon, 02 Aug 2004 14:13:06 -0400, Alexis Salas <as2444_at_columbia.edu> wrote:
> Hi, vmd -users
>
> My protein has the chargue -8 to pH 7.4. However I used autoionize the
> chargue of my system is about 0.
>
> Now i need changue the charge of my protein for the residue protonate to
> pH 7.4. How i can make this and then obtained my psf file??. I used
> charmm27.
>
> Exist one plugins or script for setting to different pHs??.
>
> Thanks in advance.
>
> Alexis Salas
>
>