From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 14 2021 - 08:28:38 CDT
Hello
CHARMM36 file
toppar_c36_2016_mass_orig/stream/prot/toppar_all36_prot_arg0.str contains
nonbonded for atom NRN1, as shown below
> NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
> cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
> !adm jr., 5/08/91, suggested cutoff scheme
>
!methylguanidine parameters
> HRA3 0.0 -0.0240 1.3400 ! alkane, yin and mackerell, 4/98
> HRP2 0.0 -0.0460 0.2245 ! small polar Hydrogen, charged
> systems
> HRM1 0.0 -0.0090 0.8750 ! aliphatic amines
> HRM2 0.0 -0.0100 0.8750 ! aliphatic amines
> !
> CRN1 0.0 -0.1100 2.0000 ! NMA pure solvent, adm jr., 3/3/93
> CR33 0.0 -0.0780 2.0500 0.0 -0.01 1.9 ! alkane (CT3),
> 4/98, yin, adm jr
> !
> NRC4 0.0 -0.2000 1.8500 ! deprotonated Schiff's base
> NRN1 0.0 -0.4500 2.0000 ! aliphatic amines
> NRN2 0.0 -0.0600 1.9900 ! aliphatic amines
> !end methylguanidine
>
Nonetheless, when running minimization for a system containing neutral ARG
(which includes atom NRN1), namd reports error for lacking vdW for atom NRN1
Thanks for advice on this issue
francesco pietra
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