Re: Combining parameter files from CHARMM

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Jun 15 2015 - 07:39:49 CDT

Kevin,

Sorry for confusion, try to download str file from:

http://mackerell.umaryland.edu/~kenno/cgenff/program.shtml

Branko

On 6/15/2015 2:29 PM, 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
> 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
>
> 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)
>>
>> 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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