[AMBER] PSF file generation for heme and hydrogen peroxide

From: 대학원/일반대학원 생명과학부 <ihc0213.yonsei.ac.kr>
Date: Thu, 13 Dec 2018 11:37:09 +0900

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
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Received on Wed Dec 12 2018 - 19:00:02 PST
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