Re: namd-I: Request for help in error fixing

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Mon Jul 26 2021 - 08:23:30 CDT

Hi,

     this has been discussed before
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/0236.html

     But those lines should **NOT** appear in the "_namd.str" file..
(Just checked again the file on
https://urldefense.com/v3/__http://mackerell.umaryland.edu/*kenno/cgenff/program.php*namd__;fiM!!DZ3fjg!v4-bY5vVDQ9TcUDk0ICNsaCg_8V-JD_Vm5QTFEDqlSpu70ItWxO1Zqub5ZQXWa7RIA$ )

Be sure to use the correct file (and remove the other one!)

Cheers

René

On 7/26/2021 3:07 PM, Dr. Anupama Tiwari wrote:
> Hi Ashkan,
>
> I am still getting the same error.
>
> On Sun, Jul 25, 2021 at 8:36 PM Ashkan Shekaari
> <shekaari_at_email.kntu.ac.ir <mailto:shekaari_at_email.kntu.ac.ir>> wrote:
>
> Dear friend,
> Use the file "toppar_water_ions_namd.str".
>
> ---
> ,Best
> Ashkan Shekaari
> PhD Candidate in Solid State Physics
> Department of Physics
> K. N. Toosi University of Technology, Tehran, 15875-4416,
> Iran<https://urldefense.com/v3/__https://scholar.google.com/citations?hl=en&user=LDzbXB4AAAAJ&view_op=list_works&sortby=pubdate__;!!DZ3fjg!qBxP9NbzXXXWbPocHmQzATU58DQnEFNa_CMpdVMt50ZR8amM_COVg1WIlNrH1WpIFw$>
>
> ------------------------------------------------------------------------
> *From: *"Dr. Anupama Tiwari" <anoopama.tiwari_at_gmail.com
> <mailto:anoopama.tiwari_at_gmail.com>>
> *To: *"namd-l" <namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>>
> *Sent: *Sunday, July 25, 2021 6:37:10 PM
> *Subject: *namd-l: namd-I: Request for help in error fixing
>
> Respected NAMD users,
> I got this error after implementing the namd command in power
> shell for md simulation:
>
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
> ./toppar_water_ions.str
> LINE=*set nat ?NATC*
> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
> ./toppar_water_ions.str
> LINE=*set nat ?NATC*
>
> Kindly suggest a solution.
> --
> *Regards,
> Dr.Anupama Tiwari
> *
>
>
>
> --
> *Regards,
> Dr.Anupama Tiwari
> Associate Prof.
> Acropolis Institute Of Technology & Research, Indore*

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany

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