On Fri, May 31, 2013, Teo, Theodosia Hua Swan - teohy004 wrote:
> Hello, I am having issues with creating input files for a calcium
> dependant cysteine protease (PDB entry 3DF0). The original PDB file
> contained 3 chains, and I have completely deleted chain C which was the
> co-crystallised ligand as well as all waters. Calcium ions have not been
> removed. The PDB was then put through VMD to remove all protons as per
> the usual set up. However, when the file was loaded into tleap using
> ff99SB to create the input files, the following error messages occurred.
>
> FATAL: Atom .R<ILE 25>.A<CD 20> does not have a type.
Sounds like the problem is with your VMD procedure. Files from the PDB
(including 3DF0) use the IUPAC atom naming scheme, which is CD1 (not CD) for
the atom mentioned above. Amber uses the same naming scheme as the PDB.
I'm not sure what you mean by "the usual setup", but there should be no reason
you have to remove protons (there aren't any in that PDB entry anyway).
> FATAL: Atom .R<CGLY 701>.A<OCT1 9> does not have a type.
> FATAL: Atom .R<CGLY 701>.A<OCT2 10> does not have a type.
Same problem as above: your setup script has changed the atom names from
what they were in the original PDB file. Don't do that!
...dac
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Received on Fri May 31 2013 - 05:30:03 PDT
