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From: Dave Arias (NelsonDa) (ndariaso_at_gmail.com)
Date: Mon Feb 27 2012 - 13:18:07 CST
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Hello.
I've been trying to create a PSF from the protein PDB file 1RFN. When
generating the new files (PDB and PSF) the primary structure of the protein
is affected by breaking some peptide bonds. The protein is divided into a
total of seven fragments. For example, the peptide bond is broken GLU -THR
at residue 60. I have worked with the A chain and B chain separately as
well have created the following PATCH to try to unite it but i do not waste
it.
I think the PARTCH is wrong. Also, i think there must be a solution to my
problem.
PRES GLUTHR 0.00 !linkage for the IMAGES or for joining segments
!1 refers to GLU (N TERMINAL)
!2 refers to THR (C TERMINAL)
!use in a path statement
DELETE IMPR 2C 2CA 1N 2O
DELETE IC 1N 2CA *2C 2O
IMPR 2C 2CA 1N 2O
IC 1N 2CA *2C 2O 1.3449 117.6900 180.0000 120.3000 1.2294
Does anyone know what should i do to fix it?
Thank you so much..
Dave.
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