[gmx-users] CYS1 or CYS2 not CYSH

[David]

On Thu, 2004-12-16 at 15:54 +0000, Osmany Guirola Cruz wrote:
> David wrote:
> 
> >On Thu, 2004-12-16 at 14:30 +0000, Osmany Guirola Cruz wrote:
> >  
> >
> >>Hi
> >> I am doing a peptide simuation that have CYS but by default pdb2gmx put 
> >>my CYS as CYSH and i need
> >>that CYS deprotonated(and without s-s) i read the rtp files and found 
> >>CYS1 CYS2 How can i use this residues. i probe change the pdb file (CYS 
> >>--->CYS1) but pdb2gmx says CYSH :-(

How about changing it to CYS2 ?

If that fails too you will have o make a new residue in your favorite
force field.

> >>What can i do?
> >>    
> >>
> >How about pdb2gmx -ss
> >
> >  
> >
> >>Thanks
> >>
> >>Osmany
> >>
> >>
> >>_______________________________________________
> >>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.
> >>    
> >>
> Does not work :-( , my problem is this i have a peptide C-XXXXXXX-C (not 
> ciclic)  but
> i dont want CYSH in mi gro file(i want it deprotonated and in the rtp 
> files i found CYS1
> and CYS2). i probed pdb2gmx -ss and pdb2gmx -ss -inter and does not work 
> always pdb2gmx
> put CYSH.
> 
> Osmany
> 
> 
> 
> _______________________________________________
> 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.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++