On Sun, Apr 05, 2015, Ziheng Wang wrote:
>
> The reduce_wwPDB_het_dict.txt is where it should be. I think the
> AMBERHOME variable is set correctly since all the others steps perform
> fine. I have attached the output pdb. The output in the terminal is as
> follows:
I see the problem, I think. The file you are feeding to reduce has the
residue called "SUS", but the official name of this residue is "EFZ". The
reduce library knows about EFZ but not about SUS.
If you start with the actual "sustiva.pdb" file from the tutorial, everything
will work. Note that the change from EFZ to SUS happens *after* reduce has
been run.
[Aside: it is *completely* perverse that the tutorial changes EFZ to SUS. We
should be following the PDB nomenclature. Note that, later on in the
tutorial, the EFZ -> SUS substitution has to be made in the 1FKO.pdb file,
just because the substitution was made initially. Plus, if you gave the
output of this simulation to anyone else, they would not know what "SUS" was
supposed to be, whereas EFZ is a well-documented entity that both the PDB, and
auxiliary programs like reduce, or phenix, or refmac, etc. already know what
to do with.... Gold stars are available to someone who can fix up the
tutorial to avoid this problem.]
....regards...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 05 2015 - 18:30:02 PDT
