[gmx-users] Is there a way to add protons to all the residues in a given system?

Justin A. Lemkul jalemkul at vt.edu
Tue Dec 9 02:36:45 CET 2008



Arthur Roberts wrote:
> Hi, all,
> 
> This is probably an obvious question.  I did a simulation with an ff53a6 
> force field, which lacks protons on aliphatic side chains.  I have pdb 
> coordinates for each time.  Is there a way to add protons to the 
> aliphatic side chains.  Your input is appreciated.
>

Check out the "protonate" tool.

-Justin


> Sincerely,
> Art Roberts
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



More information about the gromacs.org_gmx-users mailing list