On Tue, May 05, 2009, Jorgen Simonsen wrote:
>
> 1. The residues look fine around the residue so I don't that causes the
> problem.
I suppose you should post that portion of the PDB file. What looks "fine" to
you might still be a problem.
>
> 2. I am not able to generate prmtop where I get the following error message
> FATAL: Atom .R<ILE 277>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 303>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 314>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 328>.A<CD 20> does not have a type.
> FATAL: Atom .R<ILE 334>.A<CD 20> does not have a type.
I'm betting there are also lots of earlier messages ("adding new atom")
related to this. The PDB/IUPAC/Amber name for this atom is indeed "CD1", not
"CD". You will need to edit the PDB file to use the correct names.
...dac
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Received on Wed May 20 2009 - 14:42:23 PDT
