Hi!
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,
Samuel
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- application/octet-stream attachment: m1
- application/octet-stream attachment: pdb.1
- application/octet-stream attachment: prmtop
- application/octet-stream attachment: ptraj.in
Received on Mon Jun 14 2010 - 02:00:04 PDT
