Re: [AMBER] problems with "Could not find vdW"

From: Investigador Química <investigacion.faq.gmail.com>
Date: Wed, 8 Oct 2014 12:07:36 -0300

I'm sorry, I was wrong. The error is like in the photograph that I attached.


2014-10-08 11:51 GMT-03:00 Jason Swails <jason.swails.gmail.com>:

> On Wed, 2014-10-08 at 11:40 -0300, Investigador Química wrote:
> > Hi amber users.
> >
> > I have a problem when I trying to define an atom type in the parm99.dat
> > and leaprc.ff99SB.
> >
> > Amber not read the atom type that I defined, so I have problems like this
> > (for example):
> >
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Could not find bond parameter for: SH - SH
> > Could not find bond parameter for: SH - SH
> > Building angle parameters.
> > Could not find angle parameter: HS - SH - SH
> > Could not find angle parameter: HS - SH - SH
> > Could not find angle parameter: SH - SH - 2C
> > Could not find angle parameter: SH - SH - HS
> > Could not find angle parameter: SH - SH - 2C
> > Could not find angle parameter: SH - SH - HS
> > Could not find angle parameter: 2C - SH - SH
> > Could not find angle parameter: 2C - SH - SH
>
> You get these errors as a result of not preparing your PDB files that
> contain disulfide bonds correctly for tleap.
>
> As you can see, there are no errors about the CH and OH atom types.
> Paying close attention to the error messages can help prevent you from
> chasing down problems that don't exist.
>
> Also, if you pop one of those error messages into Google, you should be
> pointed to the appropriate solution. That's always a good thing to try
> first:
>
> Could not find bond parameter for: SH - SH
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>


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1.png
(image/png attachment: 1.png)

Received on Wed Oct 08 2014 - 08:30:02 PDT
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