[gmx-users] how to set parameter to ionize protein

[Louic Vermeer]

chiloo Laohpongspaisan wrote:
> Dear all,
>  
> If i would like to run channel protein in ionized state, how could i set 
> the parameter (which differ from normal protein) of the ionized protein.
> One of the protein sequences is as follow:
>  
> SER SER ASP PRO LEU VAL VAL ALA ALA SER ILE ILE GLY          
> ILE LEU */_HIS_/* LEU ILE LEU TRP ILE LEU ASP ARG LEU
>  
> I'd like to ionize the HIS residue, please suggest to where can i set or 
> change its parameters.

Use pdb2gmx with the option -inter. The program will ask you questions 
about the protonation state of the residues for which this is relevant.

>  
>  
> Best regards,
> Chiloo

You're welcome
Louic Vermeer

> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.