On Thu, Sep 24, 2015, Damiano Spadoni wrote:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> As you suggested, I checked my topology file with checkValidity (this
> kind of errors may due to something wrong in the .prmtop file) and it
> detected two CYS residues being within 3A distance and it suggested to
> change the name of the residues and build a disulfide bond, without
> specifying which cysteines it is referring about.
Well, you should certainly ignore the "suggestion" about disulfide bonds....
But if you have an SF4 resiude covalently connected to your protein, that
could likely be the source of the problem pmemd reports. My understanding is
that parmed should be able to fix this, but Jason knows more about this than
I do.
....dac
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Received on Thu Sep 24 2015 - 06:00:05 PDT
