structure problem

From: Ahlam Al-Rawi (ahlam_at_ksu.edu)
Date: Wed Apr 22 2009 - 12:22:29 CDT

Dear NAMD user,
I am trying to build a structure as fellow:

NTER-FLIVI.........
                                \ KKKKK-CT2
                                /
NTER-FLIVI.........

I add a patch in the topology file as fellow

PRES LEXT
ATOM CE CT2 -0.02
ATOM HE1 HA 0.09
ATOM HE2 HA 0.09
ATOM NZ NH1 -0.47
ATOM HZ3 H 0.31
DELETE ATOM HZ1
DELETE ATOM HZ2
BOND 1NZ 2C

The out put pdb file for this structure is in the attachment.
Using VMD the connection between residue I5 and residue K5 the N(1NZ) and
C (2C) cause a short bond length, as if the O and H(NH1) are connected
Please let me know what is wrong with the structure and how I can fix it.

Thanks
Ahlam


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