AMBER Archive (2004)

Subject: AMBER: average using ptraj

From: Holly Freedman (holly_at_mercury.hec.utah.edu)
Date: Thu Jul 08 2004 - 14:13:58 CDT

Hi AMBER,

I am using ptraj to get an average structure over an md trajectory for
the molecule 2-hydroxypyridine.
I am using amber 8 and the command was:

trajin
/uufs/hec.utah.edu/common/hecfs/nguyen/Holly/Scheme-5/2Opyr-6/mdcrd 1 10000
center
image center familiar
rms first mass out allatoms_rmstofirstSch-5.dat :1
average averageSch-5.pdb pdb

Residue 1 is the 2-hydroxypyridine molecule (iother residues are all
water).
Upon averaging the molecule turns into a completely different molecule
(not 2-hydroxypyridine) with a ring oxygen.
Here is the relevant part of the pdb for this molecule(waters removed):

ATOM 1 C1 MOL 1 -0.490 -1.401 -0.183 0.00 0.00
ATOM 2 H4 MOL 1 -1.024 -2.244 -0.336 0.00 0.00
ATOM 3 C2 MOL 1 0.889 -1.506 0.021 0.00 0.00
ATOM 4 H1 MOL 1 1.284 -2.513 0.015 0.00 0.00
ATOM 5 C3 MOL 1 1.595 -0.312 0.211 0.00 0.00
ATOM 6 H2 MOL 1 2.661 -0.347 0.372 0.00 0.00
ATOM 7 C4 MOL 1 0.948 0.916 0.223 0.00 0.00
ATOM 8 H5 MOL 1 1.503 1.826 0.390 0.00 0.00
ATOM 9 N1 MOL 1 -0.422 0.956 0.019 0.00 0.00
ATOM 10 C5 MOL 1 -0.994 1.871 0.003 0.00 0.00
ATOM 11 O1 MOL 1 -1.216 -0.284 -0.221 0.00 0.00
ATOM 12 H3 MOL 1 -2.440 -0.335 -0.474 0.00 0.00

Here is the pdb of 2-hydroxypyridine:

ATOM 1 C1 MOL 1 17.134 18.235 15.519
ATOM 2 H4 MOL 1 16.605 19.181 15.519
ATOM 3 C2 MOL 1 18.519 18.153 15.519
ATOM 4 H1 MOL 1 19.117 19.060 15.521
ATOM 5 C3 MOL 1 19.138 16.895 15.519
ATOM 6 H2 MOL 1 20.217 16.796 15.518
ATOM 7 C4 MOL 1 18.323 15.770 15.519
ATOM 8 H5 MOL 1 18.755 14.770 15.520
ATOM 9 N1 MOL 1 16.982 15.824 15.519
ATOM 10 C5 MOL 1 16.417 17.029 15.519
ATOM 11 O1 MOL 1 15.065 17.078 15.519
ATOM 12 H3 MOL 1 14.767 16.154 15.518

I believe that this has to be caused by a bug in the ptraj program. The
resulting pdb file shows a molecule but not the same one I started with,
which does not seem to result from overlapping molecules being averaged.
Your help would be very much appreciated.
Thanks in advance,

--Holly Freedman,
   University of Utah

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