From: Grace Brannigan (gracebrannigan_at_gmail.com)
Date: Wed Sep 18 2013 - 11:59:02 CDT
Hi Anna,
The OT atom type is in the TIP3P model for water. If you are using
charmm36 you will need to include the toppar_water_ions.str file in your
parameters listed in the configuration file. Then you will get another
error (I think) which can be solved by commenting out charmm commands as in
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21783.html
cheers,
Grace
On Wed, Sep 18, 2013 at 11:01 AM, Anna Chailyan <anna.chailyan_at_gmail.com>wrote:
>
> Hello Hello!
>
> I am desperate !
>
> Today i made a new psf file with topology topology top_all36_prot.rtf
> and topology top_all36_na.rtf since my complex is made of protein and dna.
> It runs fine and i obtain the psf file.
> I attached the configuration file
>
> .
> It keeps crashing when i run minimization by saying "FATAL ERROR: DIDN'T
> FIND vdW PARAMETER FOR ATOM TYPE OT".
>
> I don't know, which are the possibilities.
>
>
>
> Best Regards,
>
>
> On Sep 18, 2013, at 1:20 AM, Kenno Vanommeslaeghe <
> kvanomme_at_rx.umaryland.edu> wrote:
>
> 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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