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

From: zeynab hosseini (
Date: Wed Sep 02 2020 - 07:03:11 CDT

Hi Josh,

Thank you for the prompt reply. As I compared the 2020 version of the
mentioned .str file with the available NAMD format one (which is on 2016),
the new one contains some new updates on "Calcium and Potassium NBFixes"
which was added on 2019-8. It also include some other changes that I don't
know what they are exactly.

As you said I commented the commands that NAMD does not understand in the
new .str file and it is working now. Since I don't know what those commands
do, I'm a little bit concerned about commenting them. Do you know if this
removal would affect the physical outcome of the MD simulation?

All the Best,

On Sun, Sep 13, 2020 at 2:14 AM Josh Vermaas <>

> 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.
> -Josh
> On Fri, Sep 11, 2020 at 10:59 PM zeynab hosseini <
>> wrote:
>> 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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