From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jun 15 2015 - 11:10:43 CDT
Basically you take a standard toppar_water_ions.str and remove the lines
that CHARMM understands but NAMD doesn't. This means all residue
definitions need to be deleted, as well as lines that are specific to
CHARMM (like "return" or "if", which control flow in CHARMM). Just be
careful at the bottom near the NBFIX lines, as they can cause problems
if other parameter files that define the atomtypes that sodium has a
special interaction with aren't loaded in first.
-Josh Vermaas
On 6/15/15 7:29 AM, Kevin C Chan wrote:
> Thanks for the reply.
>
> I have tried but I don't think charmm-GUI would give the file, either
> nor the tgz downloaded directly from CHARMM.
>
> Thanks in advance,
> Kevin
>
> On Mon, Jun 15, 2015 at 5:37 PM, Branko <bdrakuli_at_chem.bg.ac.rs
> <mailto:bdrakuli_at_chem.bg.ac.rs>> wrote:
>
> Kevin,
>
> Try to make parameters with charmm-GUI:
> http://www.charmm-gui.org/?doc=input
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.charmm-2Dgui.org_-3Fdoc-3Dinput&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=DIcSqEq0eE00unc_s3MIvGeTyO3ftF5HKFeg5R7RUBM&s=_oxIG7BIjwI31e6Yqqy55YbLQqYEb2AvJ0Guslv4vmg&e=>
>
> Chose some small protein and solvate such system. Among parameters
> generated you can find this str file.
> Alternatively, check could this file can be found in
> 'toppar_c36_aug14.tgz' on
> http://mackerell.umaryland.edu/charmm_ff.shtml
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__mackerell.umaryland.edu_charmm-5Fff.shtml&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=DIcSqEq0eE00unc_s3MIvGeTyO3ftF5HKFeg5R7RUBM&s=RIoLFyMLGYCMXZ54Mdqt6a3-DG1hMmez1imc1HhEIIU&e=>
>
> Branko
>
>
> On 6/15/2015 10:07 AM, Kevin C Chan wrote:
>> Thanks Branko. It works perfectly fine until I met the stream
>> files, e.g. toppar_water_ions.str. I looked back the thread and
>> found you have already given hints on it. So how did you get that
>> toppar_water_ions_namd.str? By deleting those CHARMM languages
>> one by one?
>>
>> Thanks,
>> Kevin
>>
>> On Fri, Jun 5, 2015 at 6:17 PM, Branko <bdrakuli_at_chem.bg.ac.rs
>> <mailto:bdrakuli_at_chem.bg.ac.rs>> wrote:
>>
>> Kevin,
>>
>> You not need to have single parameter file for NAMD
>> simulation, just specify parameters in namd configuration
>> file, for example:
>>
>> parameters par_all36_carb.prm
>> parameters par_all36_cgenff.prm
>> parameters par_all36_lipid.prm
>> parameters par_all36_na.prm
>> parameters par_all36_prot.prm
>> parameters toppar_water_ions_namd.str - pay attention on
>> this line. CHARMM36 water and ions parameters for NAMD
>>
>> Alternatively you can use inp merge, built-in in VegaZZ
>> (http://nova.disfarm.unimi.it/cms/index.php?Software_projects:VEGA_ZZ
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__nova.disfarm.unimi.it_cms_index.php-3FSoftware-5Fprojects-3AVEGA-5FZZ&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=DIcSqEq0eE00unc_s3MIvGeTyO3ftF5HKFeg5R7RUBM&s=P8oB4XU4of5rEYUNZPdz8k9lp1HG6l-FSbrAYhQ560I&e=>)
>>
>> Branko
>>
>>
>> On 6/5/2015 11:51 AM, Kevin C Chan wrote:
>>> Dear Users,
>>>
>>> I guess there will be a quick answer. I am wondering how
>>> people usually combine parameter files directly downloaded
>>> from CHARMM website to have the par_all36_XXX.inp? For
>>> instance, we want to combine all the parameter files from
>>> CHARMM36 to become one single inp to be read for my NAMD
>>> simulation.
>>>
>>> Thanks in advance,
>>> Kevin
>>> City University of Hong Kong
>>
>>
>
>
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