Dear all,
>From each snapshot of a protein/ligand simulation, I want to generate a pdb file containing the protein, ligand and waters/ions within a certain distance from the protein and ligand. I have tried to use ptraj to strip waters/ions beyond this distance. (I use Amber10 and AmberTools-1.2.)
I have tried the following
trajin 1.crd
reference 1.crd
strip (:1-107 >. 6.0)
trajout 1.pdb PDB
go
inspired by the thread
http://archive.ambermd.org/200806/0162.html, where 1.crd is the coordinate file for the first snapshot.
However, I receive the following message
-----------------------------------------------------------
PTRAJ: Processing input from "STDIN" ...
PTRAJ: trajin 1.crd
Checking coordinates: 1.crd
PTRAJ: reference 1.crd
Processing AMBER trajectory file 1.crd
PTRAJ: strip (:1-107 >. 6.0)
ERROR in parsing atom mask: unbalanced parentheses in expression
------------------------------------------------------------------------------------
If I remove the parentheses, i.e. use strip :1-107 >. 6.0, it only reads :1-107 and thus it strips the protein/ligand. As far as I can see, the problem is the distance-criterium since removing that, i.e. using strip (:1-107), works but does not give the desired result.
I have also tried using
"(:1-107 >. 6.0) "
'(:1-107 >. 6.0)'
":1-107 >. 6.0 "
[:1-107 >. 6.0]
but receive a "segmentation fault".
Any help is much appreciated.
Best regards,
Nanna H. List
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Received on Tue Feb 28 2012 - 12:00:02 PST
