AMBER Archive (2002)

Subject: average structure

From: Raja Swaminathan (rajaamber6_at_rediffmail.com)
Date: Thu Sep 05 2002 - 12:16:03 CDT

Hi

I have done a 2ns MD on an unusual DNA duplex. for average
structure analysis i have used the following inputs

this is the first one

/home/programs/amber6/exe/ptraj dat6_nowat.top << EOF
trajin dat6_nowat_final.stripped.Z (without any water or ions)
average average2ns.pdb pdb
go
EOF

second is

/home/programs/amber6/exe/ptraj dat6_nowat.top << EOF
trajin dat6_nowat_final.stripped.Z
center :1-14 mass origin
image origin center
center :1-28 mass origin
image origin center
average average2ns_1.pdb pdb
go
EOF

in both the cases i have used the imaged file as inputs. in both
the cases i get two different pdb coordinates. rms between the two
structure varies by about 0.7 A.

why it is so. in both the cases i am using the same inputs, if i
try to image once again the stripped files i am facing this
problem.

Thanking u in advance

Sincerely
Raja Swaminathan