From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Sun Sep 13 2020 - 10:47:16 CDT
Thank you very much for the explanation...
All the best, Z.
On Sun, Sep 13, 2020 at 8:15 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:
> 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.
> Josh
>
> On Sun, Sep 13, 2020, 12:59 AM zeynab hosseini <hosseinizeynab93_at_gmail.com>
> wrote:
>
>> 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 <joshua.vermaas_at_gmail.com>
>> 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 <
>>> hosseinizeynab93_at_gmail.com> 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:
>>>>
>>>> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
>>>> 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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