wrong pdb struvture generated while using patch

From: hem_chandra_at_iitg.ernet.in
Date: Fri Apr 07 2017 - 02:06:11 CDT

Hello NAMD users,

   As per the user manual I am trying to generate a pdb and psf files. But
while using the patch command to the N-terminus the branch chain of the
(to be patched molecule) gets distorted and adds up to a different
atoms.

However the C-terminal patch seems to be Okay.

myfile.pgn :
https://drive.google.com/open?id=0B77lRAKVhq_RM3lzUGJ4bmtlSzQ
wwl.pdb
https://drive.google.com/open?id=0B77lRAKVhq_RWnFocTZXRUJYNGc

top_all36_cgenff containig all the contents of BOC molecule:
https://drive.google.com/open?id=0B77lRAKVhq_RWnA3clY1Z1R1czA

top_all_36_prot: cotaining CT1
https://drive.google.com/open?id=0B77lRAKVhq_RQ3FfWWRoWjhGY1k

Thanking with anticipation
_hemchandra

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