Re: Error

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Mon Oct 21 2013 - 12:17:41 CDT

- Do not send questions per personal e-mail. See recent rants.

- In the CHARMM force field, "OT" stands for O(TIP3), so it appears your
PSF contains TIP3 water. *Technically* spoken, if you want to use SPC/E
water, you need to generate a PSF with SPC/E water. *HOWEVER*, the CHARMM
additive force field is parameterized against TIP3 and will not
necessarily yield balanced interactions when combined with other water
models. As an exception, we did recently get good results using CHARMM
with TIP5P, so if that model suits your purpose, it would probably be safe
to use (though validation for your specific purpose is always
recommended). Also, we're right now finalizing the first official public
release of the CHARMM Drude polarizable force field, which works with NAMD
and is parameterized against SWM4-NDP, so if you have the luxury to wait
for it, you could try that one.

On 10/19/2013 01:10 PM, Mihaela Drenscko wrote:
> Hi,
>
> I followed the above instructions, but the simulation doesn't work.
> I'm using SPCE water model, so I can't use topar_water_ions_namd.str. Here
> is the input I am using:
>
> # Input
> paraTypeCharmm on
>
> parameters wg.inp
> parameters par_all36_prot.prm
> mergeCrossterms yes
> parameters par_all36_lipid.prm
> parameters par_all36_carb.prm
> parameters par_all36_cgenff.prm
>
> And when I run the simulation with namd,
> I still get the same error,
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> 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
>
> Aborted (core dumped)
>
> How do I fix it?
>
> Thank you,
>
> Mihaela
>
>
>
>
>
>
> On Wed, Oct 16, 2013 at 10:21 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> Please note that the NAMD list has an archive that can be searched;
> this exact question is being asked about once a week on average.
>
> http://mackerell.umaryland.__edu/~kenno/cgenff/program.__html#namd
> <http://mackerell.umaryland.edu/%7Ekenno/cgenff/program.html#namd>
> (if you don't have a CGenFF molecule, omit the molecule.str line)
>
>
>
>
> On 10/16/2013 09:15 PM, Mihaela Drenscko wrote:
>
> Hello,
>
> I was running a namd simulation, when I got this error:
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OT
>
> How do I fix it?
>
> Thank you,
>
> Mihaela
>
>
>

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