[AMBER] Ptraj problems

From: Samuel Genheden <samuel.genheden.gmail.com>
Date: Mon, 14 Jun 2010 10:47:25 +0200

We have had much problems with wrapping with ptraj.
Here is an example, where we try to centre on the first atom and wrap
into an octahedral box, but we get a number of waters at a distance and
therefore also a wrong centering.

ptraj.in is the ptraj input file
prmtop is the prmtop file
m1 is the mdcrd file (just a single snapshot)
pdb.1 is the wrapped result

Can somebody help us?

We have been trying with many versions of ptraj, including the one in
AmberTools 1.4

Best regards,

AMBER mailing list

Received on Mon Jun 14 2010 - 02:00:04 PDT
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