From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri May 09 2014 - 11:50:45 CDT
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I'm starting to feel like a broken record here.
To answer the question, CHARMM36 has been modularized, which means that
not only the topolgy for ATP is in stream/toppar_all36_na_nad_ppi.str ,
but also its parameters. Consequently, said file needs to be read into
NAMD in order for it to have all the necessary parameters.
On 05/09/2014 11:40 AM, Andreas Förster wrote:
> Dear Kenno,
>
> I've followed the instructions below on how to use Charmm36 with NAMD.
>
> I've created a fresh psf file from a protein with bound ATP. No problem.
> Running vacuum minimization produces an "UNABLE TO FIND ANGLE PARAMETERS
> FOR P ON2 P2" error. I look for this angle in par_all36_na.prm, but it's
> not there.
>
> In Charmm36,
>
> grep ON2 *.prm | grep P2 | grep " P "
>
> returns nothing.
>
>
> in Charm27,
>
> grep ON2 *.prm | grep P2 | grep " P "
>
> returns
>
> P2 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95
>
> in par_all27_na_lipid.prm, par_all27_na.prm and par_all27_prot_na.prm.
>
>
> What am I missing? Should I just copy this line to the appropriate place
> in par_all36_na.prm?
>
> Thanks for your advice.
>
>
> Andreas
>
>
>
>
>
>
>
>
> On 23/04/2014 6:28, Kenno Vanommeslaeghe wrote:
>> - I don't think NAMD itself can read topology (rtf) files
>> - You cannot use an old psf with the new parameter (prm) files; you'll
>> have to regenerate the psf (with psfgen, VMD, CHARMM-GUI,...) based on
>> the new topology (rtf) files
>> - In release 36, we made the CHARMM force field modular, with water
>> being in a separate stream file. Unfortunately, this modularity doesn't
>> work in NAMD. The recommended workaround is to use a NAMD-specific
>> version of the water stream file ( toppar_water_ions_namd.str ) *and* to
>> *always* read *all* parameter files, even if they're not needed for a
>> given simulation. See
>> http://mackerell.umaryland.edu/~kenno/cgenff/program.html#namd
>> - If the above doesn't solve your problem, please give more details.
>> "NAMD crashing" is exceedingly vague and makes me feel like I shouldn't
>> help you.
>>
>>
>> On 04/23/2014 12:15 PM, Alex Utev (CMP) wrote:
>>> Hi,
>>>
>>> I've recently downloaded the CHARMM36 force field to use with NAMD. I
>>> believe the 2 main files
>>> are the "par_all36_prot.prm" file and the "top_all36_prot.rtf" file.
>>> Previously just adding the files using
>>> the parameters field seemed to work but with the new v36 files this
>>> seems to result in NAMD crashing.
>>> Any ideas what the issue is?
>>>
>>> Alex Utev
>>>
>>>
>>
>>
>
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