From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 14 2021 - 08:46:04 CDT
I notice now from the terminal window that the stream file
toppar_all36_prot_arg0.str , although present, was not read
Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS ./par_all36_lipid.prm
> Info: PARAMETERS ./par_all36_prot.prm
> Info: PARAMETERS ./par_all36_na.prm
> Info: PARAMETERS ./par_all36_cgenff.prm
> Info: PARAMETERS ./ligand.str
> Info: PARAMETERS ./par_water_ions.prm
>
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> Info: SKIPPING rtf SECTION IN STREAM FILE
>
No warning was reported about the params for the ligand, but it might be
that namd halted at the first issue, before the stream file for the ligand
was read
Again, thanks for advice
francesco pietra
---------- Forwarded message ---------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Sep 14, 2021 at 3:28 PM
Subject: vdW for atom NRN1
To: NAMD <namd-l_at_ks.uiuc.edu>
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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