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

From: Josh Vermaas (
Date: Sun Sep 13 2020 - 10:45:31 CDT

Those commands control how charmm parses the file (reads parameters and/or
topology), but don't impact dynamics. That is why removing them so the NAMD
parser works is fine.

On Sun, Sep 13, 2020, 12:59 AM zeynab hosseini <>

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

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:14 CST