Fwd: Re: Combining parameter files from CHARMM

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Jun 15 2015 - 05:12:57 CDT

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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