Re: toppar_water_ions.str NAMD format for last version of C36 (on July 2020)

From: Josh Vermaas (
Date: Sat Sep 12 2020 - 16:44:27 CDT

Hi Zeynab,

Just yank out the stuff NAMD doesn't understand. I make my own parameter
files by only keeping the parameter information in the toppar file. To be
honest, did anything in the water or ions parameters change with the July
version? I'm almost positive you'll find that the parameters will be
identical to the old ones.


On Fri, Sep 11, 2020 at 10:59 PM zeynab hosseini <>

> Dear all
> I want to use CHARMM36 (the latest version on July2020) to perform MD
> simulation utilizing NAMD. The problem is that the "standalone stream file
> for water and ions" (toppar_water_ions.str) for the latest version of C36
> is not available in the NAMD format.The only available namd format
> (toppar_water_ions_namd.str) does not contain the latest updates in the
> last version of toppar_water_ions.str for C36(July 2020). Is there any way
> that I can convert the .str file in the CHARMM format to the NAMD one? Or
> any other suggestion?
> As soon as I run the MD simulation with the latest toppar_water_ions.str,
> I receive the following error massage:
> toppar_c36_jul20/toppar_water_ions.str
> LINE=*set nat ?NATC*
> Would be grateful if somebody guide me..
> All the best,
> Zeynab

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