From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Sep 17 2013 - 18:20:38 CDT
We recommend using the new CHARMM36 force field, which has significant
improvements, and has been made modular (ie. no more need to merge
parameter files). The force field can be downloaded from
http://mackerell.umaryland.edu/CHARMM_ff_params.html
Note that PSFs generated using the old force field usually won't work with
the new one; one has to feed psfgen the new topology files from the force
field distribution package. So assuming your system contains protein,
lipids and water, Niklaus' recommendations for psfgen would become:
topology top_all36_prot.rtf
topology top_all36_lipid.rtf
topology toppar_water_ions.str # not sure it will accept this
and for NAMD:
paraTypeCharmm on
parameters par_all36_prot.prm
parameters par_all36_lipid.prm
parameters toppar_water_ions.str
Cheers,
Kenno.
PS. For the record, the vintage *_all27_prot_lipids.* files were a merger
of the CHARMM22 + CMAP protein force field and the CHARMM27 lipid force
field, so the below methodology would have you read in obsolete CHARMM27
lipid definitions and parameters, then overwrite them with CHARMM36 ones.
While I'm not sure this is a problem, it seems a bit risky.
On 09/17/2013 12:35 PM, Niklaus Johner wrote:
> This looks like you didn't load the proper parameter files when running
> your simulations.
>
> Typically when you generate your psf with psfgen (I guess?), you input
> some topology files for example:
>
> topology top_all27_prot_lipids.rtf
> topology top_all36_lipid.rtf
>
> So then in your namd input you need to load the cognate parameter files.
> Something like:
>
> paraTypeCharmm on
> parameters par_all27_prot_lipids.prm
> parameters par_all36_lipid.prm
>
> Otherwise some of the atoms defined in your psf file won't be defined in
> the parameter files.
>
> N.
>
>
> Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
>
>
>
> On Sep 17, 2013, at 12:10 PM, Anna Chailyan wrote:
>
>>
>> Help!
>>
>> After all the previous successful steps finally i have psf file of my
>> complex and now when i try to minimize it i get this message:
>>
>>
>>
>> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
>>
>> Charm++ fatal error:
>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
>>
>>
>> I am using NAMD_2.9_MacOSX-x86_64-multicore and i wonder why do i get
>> this message now, not when i actually generated psf file.
>> Please ! if there is someone that got this problem and knows how to
>> solve it, share it with me!
>> Best regards,
>> Anna
>
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