VMD-L Mailing List

From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Tue Feb 15 2005 - 18:16:00 CST

Hi:

If you have D & E protonated, they are defined as ASPP and GLUP on your
pdb/psf, right??

I think that you will need to:

1. save a new pdb without hydrogens
2. generate a new psf file using aliases:

alias residue GLUP GLU
alias residue ASPP ASP

Now you have unprotonated D & E residues!!!
Dont forget to write new pdb/psf files...

Hope this helps,

Ludwig 

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---------- Original Message -----------
From: Gaurav Sharma <sharma_at_coe.neu.edu>
To: vmd-l_at_ks.uiuc.edu
Sent: Tue, 15 Feb 2005 11:42:06 -0500
Subject: vmd-l: Unprotonating GLU, ASP
> Hi All,
> 
> I used the psfgen's patch command to protonate GLU, ASPs to study 
> the effect of lower pH. Is there a similar patch command to un-
> protonate the GLU, ASP in the final structure obtained from the 
> above simulation in order to study the reversibility of the reaction.
> 
> Thanks in advance,
> 
> Gaurav
------- End of Original Message -------