Tutorial-l Mailing List

From: 대학원/일반대학원 생명과학부 (ihc0213_at_yonsei.ac.kr)
Date: Wed Dec 12 2018 - 20:35:20 CST

Dear, all NAMD users and supporters,

I would like to simulate catalase proteins which have heme d and hydrogen
peroxide, with NAMD.
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,
and know how to modify my configuration file for NAMD to use the parameter
for heme.

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 simulate NAMD
with the psf files.
(I could not 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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