From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Tue Sep 14 2021 - 08:53:17 CDT
Dear friend,
This is because
* you have not correctly added the path of toppar_all36_prot_arg0.str in your input file; or
* you have not added the path of toppar_all36_prot_arg0.str in your input file; or
* the file toppar_all36_prot_arg0.str is not a readable ASCII file.
---
,Best
Ashkan Shekaari
PhD Candidate in Solid State Physics
Department of Physics
K. N. Toosi University of Technology, Tehran, 15875-4416, Iran [ mailto:shekaari_at_email.kntu.ac.ir ] [ https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!otVH2KFC0w-5BSzWV3DfSN3DpH80KjI6gtfb7R70CExjmuQfu8hAFb0LW0ochqhjSg$ ]
From: "Francesco Pietra" <chiendarret_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Sent: Tuesday, September 14, 2021 5:58:38 PM
Subject: namd-l: vdW for atom NRN1
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
BQ_BEGIN
!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
BQ_END
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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