Hi,
The distance-based mask parsing syntax can be a little tricky. To keep
all atoms within 6 angstroms of residues 1-107 try:
strip !(:1-107<.6.0)
Note however that in ptraj distance-based masks are set up only once
based on the reference coordinates. The mask does not update over each
frame, so in order for the mask to be accurate you would need to read
in each frame one at a time, using that frame as a reference.
In the next release of AmberTools (coming within the next few months)
cpptraj will have a command called 'mask' that does exactly what you
describe:
mask (:1-107<.6.0) maskpdb mask.pdb
will generate a series of PDB files named mask.pdb.X for all atoms
within 6 angstroms of residues 1-107, updated each frame.
-Dan
On Tue, Feb 28, 2012 at 2:52 PM, Nanna Holmgaard List
<nalis07.student.sdu.dk> wrote:
> 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 - 15:00:02 PST
