Dear, all AMBER users and supporters,
I would like to simulate catalase proteins which have heme d and hydrogen
peroxide, with AMBER. I use VMD to make psf (protein structure file) from
pdb, but I could not find topology file for heme and hydrogen peroxide.
I only found 'toppar_all36_prot_heme.str' in CHARMM force field parameters,
However, I could not find parameter files for hydrogen peroxide.
I could not even make psf file for catalase proteins without hydrogen
peroxide using VMD.
I think I may get error messages from VMD, because I don't have topology
file for heme.
What should I do for finding parameter files and making psf files for
catalase proteins.
Additionally, I wonder how to make psf file from other softwares, not VMD.
I know 'Discovery Studio' can make psf file, but I failed to be over charmm
parameter errors)
Thank you for your kindness!
Respectfully yours,
>From Hocheol Lim, Graduate Student in the Master's course
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 12 2018 - 19:00:02 PST
