I have attached the topology file and the restart file for one snapshot. Thanks a lot.
I will upgrade to AmberTools version 1.5 and try with this as well.
Best regards,
Nanna
________________________________________
Fra: Daniel Roe [daniel.r.roe.gmail.com]
Sendt: 29. februar 2012 15:10
Til: AMBER Mailing List
Emne: Re: [AMBER] strip and use of distance-based mask
Hi,
The distance-based mask works for me in ptraj for AmberTools 1.2 and
1.5, so it might be there is something specific to your system that is
triggering the segfault. Could you provide me with a topology file and
a restart so I can try and reproduce the problem? Thanks.
That said, I would strongly recommend that you upgrade to the latest
version of AmberTools (1.5) and apply all bugfixes. There are many
improvements to the code and issues that have been fixed since version
1.2.
-Dan
On Wed, Feb 29, 2012 at 1:42 AM, Nanna Holmgaard List
<nalis07.student.sdu.dk> wrote:
> Thanks for the reply.
>
> When I use
>
> strip !(:1-107<.6.0)
>
> I receive "segmentation fault", so I was wondering whether it is possible with the current strip to use a distance-based mask at all?
>
> Best regards,
>
> Nanna
> ________________________________________
> Fra: Daniel Roe [daniel.r.roe.gmail.com]
> Sendt: 28. februar 2012 23:48
> Til: AMBER Mailing List
> Emne: Re: [AMBER] strip and use of distance-based mask
>
> 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
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 29 2012 - 09:00:02 PST
