From: DimitryASuplatov (genesup_at_gmail.com)
Date: Sat Apr 25 2009 - 08:56:05 CDT
Am I correct that I should introduce new entry to charmm topology file like
ATOM DEFINE CG_CYS and CX_TYR
On Sat, Apr 25, 2009 at 5:23 PM, DimitryASuplatov <genesup_at_gmail.com> wrote:
> I have a covalent bond between Tyr and Cys in my structure. I want to
> preserve this bond for molecular dynamics.
> I was recently using GROMACS. So to introduce this bond I had to
> 1/ Specify the atom-atom distance for this bond in specbond.dat file.
> In case of such distance occurs Cys2 and Tyr2 topologies are used
> instead of Cys and Tyr default ones.
> 2/ Specify new protonation state for Tyr2 residue in ff protonation file
> 3/ Write a new topology to ff topology file file
> Could you briefly associated those stages to NAMD?
> I appreciate your time.
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