From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 14 2021 - 09:26:02 CDT
You are rigth, but, to make the story short, I extracted the parameters
from the stream file and now namd is happy
thanks
francesco
On Tue, Sep 14, 2021 at 3:53 PM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:
> 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
> <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!u0S3x2aeyVgPyPlBjOGxrrHixfkBy3rrl0VJvj_YompyYUZdEj_HBHgfHeKNi6ujbA$ >
>
> ------------------------------
> *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
>>
> !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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