Hi,
On Tue, Mar 10, 2015 at 3:54 AM, Anasuya Dighe
<anasuya.mbu.iisc.ernet.in> wrote:
> ----------
> 1uh7-wat-md801.crd (1-500, 1)
> 0% Warning: For PDB, box coords for first frame only will be written to CRYST1.
> Warning: Frame 11 coords 1 & 2 overlap at origin; may be corrupt.
The trajectory frames in question are either partially or fully
corrupt and cannot be used (I'll explain more below if you're
interested). They can be excluded by using the 'check' command with
'skipbadframes', e.g.
trajin 1uh7-wat-md801.crd
check .1,2 skipbadframes silent nobondcheck
What is happening here is that cpptraj always does a relatively
inexpensive check of coordinates as they are read in to see if the
first two atoms have the coordinates {0,0,0}, i.e. they overlap at the
origin, which will only happen if the trajectory has been corrupted in
some way (or you're using some crazy force field I suppose). So of
course the RMSD of a structure from your reference to having most or
all coordinates suddenly located at the origin is going to be very
high. The 'check' command I wrote above checks those same two atoms
(but for safety's sake you should probably change the mask to check at
least any atoms you want to perform analysis on) and the
'skipbadframes' option tells cpptraj to not continue processing the
frame if problems are found.
Hope this helps,
-Dan
> Warning: Frame 12 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 13 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 14 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 15 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 16 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 17 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 18 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 19 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 20 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 21 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 22 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 23 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 24 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 25 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 26 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 27 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 28 coords 1 & 2 overlap at origin; may be corrupt.
> Warning: Frame 29 coords 1 & 2 overlap at origin; may be corrupt.
> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----------
> Are these two issues related ?
> What seems to be going wrong here in the simulation? What can i do to rectify
> this error?
> Please help.
>
> Regards,
> Anasuya Dighe
> Indian Institute of Science,
> Bangalore,
> INDIA
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 10 2015 - 07:30:04 PDT
