RE: AMBER: average using ptraj

From: Ross Walker <>
Date: Thu, 8 Jul 2004 13:18:58 -0700

Dear Holly,

> 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,

I'm not sure how a bug in ptraj could have done this since it all it does is
average the coordinates. The chances of a bug in such averaging morphing
into a different molecule are extremely slim. I suspect more is at play
here. A few questions:

1) Are you certain you simulated the correct molecule? If you create a pdb
from your starting prmtop and inpcrd (or restrt) file what does it look

ambpdb -p prmtop < inpcrd > start.pdb

Does this look correct?

2) What happens if you don't average in ptraj, say just write out the first
set of coordinates from the mdcrd file as a pdb?

3) What about visualising the mdcrd file in something like VMD, does it look
correct here?

4) Are you running classical MD or QMMMMD?

If all of the above give you what you want then please let me know and I
will try and investigate further.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Thu Jul 08 2004 - 21:53:00 PDT
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