From: Mohammad Mehdi Pirnia (mpdezfouli_at_gmail.com)
Date: Tue Sep 14 2021 - 09:25:54 CDT
Hi Francesco,
Once I faced a rather similar error. My source of forcefield files was my
output from a source other than the CHARMM-download page. So, I downloaded
the whole version from the CHARMM-download page and copied my str file in
the right directory from which the vmd was reading toppar files. Hope this
helps your problem gets addressed.
Bests,
Adam
On Tue, Sep 14, 2021 at 6:17 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:
> 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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