Tutorial-l Mailing List

From: Aurijit Sarkar (sarkara_at_vcu.edu)
Date: Thu Sep 24 2015 - 14:41:36 CDT

Hi all,

I need to perform some FEP calculations for a protein-sugar complex using
CHARMM36-based carbohydrate parameters. Problem is, the hybrid topology
file supplied with NAMD for amino acid mutation is compatible with CHARMM22
but not CHARMM36. For example, it provides the atom name HA for all
hydrogens bonded to CT2 or CT3 atoms, whereas in CHARMM36 these are
supposed to be called HA2 and HA3 respectively.

One possible solution is to use CHARMM22 protein parameters and CHARMM36
carbohydrate parameters together. Can I safely do this?

If not, does anybody have a hybrid topology file based on CHARMM36 so I
don't have to mix and match?

Any help provided will be highly appreciated, thanks!

Cheers,

Auri 

-- 
Aurijit Sarkar, PhD
Department of Medicinal Chemistry &
Institute for Structural Biology, Drug Discovery & Development,
Virginia Commonwealth University,
800 E. Leigh St. Suite 212, Biotech One,
Richmond, VA 23219-1540
USA
Phone: (804) 938-5543
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