Hello Charmm users,

I'm trying to model a lactose molecule using drude force field. I found that I need to use PATCH command to add a new bond between galactose and glucose. The command I used are follows

stream toppar_drude_master_protein_2013e.str
stream toppar_drude_carbohydrate_2013e.str
stream toppar_drude_model_2013e.str
open read card name "lactose.pdb" unit 21
read sequence pdb unit 21
generate CARB first none last none setup warn drude dmass 0.4
patch 14BA CARB 2 CARB 1 setup warn

The error message shows ' ERROR in PATIC: Residue 14BA was not found.' It is confusing since 14BA is just patch name not residue ID. The exact PATCH command worked when using regular charmm36 forcefield such as following:

open read card name "top_all36_carb.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36_carb.prm" unit 25
read parameter card unit 25 flex
close unit 25

open read card name "lactose.pdb" unit 21
read sequence pdb unit 21
generate CARB first none last none setup warn
!! 1beta galactose link 4alpha glucose
patch 14BA CARB 2 CARB 1 setup warn

I suspect it relates with DRUDE topology
I appreciate any help.
Thank you

Last edited by Allen_123; 11/21/19 09:15 AM.