AMBER Archive (2005)

Subject: AMBER: nucgen problem

From: cbala_at_igib.res.in
Date: Tue Jun 07 2005 - 08:41:27 CDT

hello,

i have two questions on constructing pdb files

1) i constructed a 12mer DNA duplex using 'nucgen' program. the program
runs fine and it has successfully created the pdb file but when i view
the pdb file, overlapping of bases is seen at some base pairs, 4 out of
12 base pairs, it occurs in both GC and AT pairs, can anyone suggest
what could be the reason for this and how i can avoid it.

2) i constructed a B-DNA duplex (10 mer) in insightII and i loaded in
xleap after deleting all hydrogens, but xleap adds one phosphite at the
5' positions of both the strands, can anyone help in solving this
problem.

thanks in advance,
c.bala
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