From: Teerapong Pirojsirikul (tpirojsi_at_mail.ucsd.edu)
Date: Wed Sep 18 2013 - 12:20:24 CDT
Hi,
I saw you commented out toppar_water_ions.str which is required for
the OT atom type. It seems to me that OT atom type is for TIP3P
oxygen. My guess is you also used this file in psfgen and your system
is solvated with TIP3P water, right?. However, I found it's a little
bit tricky to also use this file in a namd configuratoin file. You
need to delete or comment out a bunch of lines in it. I'd recommend
trying my modified toppar_water_ions.mod.str attached. Just put it in
your working directory and fix the line
paraTypeCharmm on
parameters ./par_all36_prot.prm
parameters ./par_all36_na.prm
#parameters ./toppar_water_ions.str
to
paraTypeCharmm on
parameters ./par_all36_prot.prm
parameters ./par_all36_na.prm
parameters ./toppar_water_ions.mod.str
,and give me feedback.
Cheers,
Tee
2013/9/18 Anna Chailyan <anna.chailyan_at_gmail.com>:
>
> 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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