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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Received on Wed Oct 08 2014 - 08:00:03 PDT
