Thank you very much for your help, Dan.
Best regards,
Nanna
________________________________________
Fra: Daniel Roe [daniel.r.roe.gmail.com]
Sendt: 29. februar 2012 18:23
Til: AMBER Mailing List
Emne: Re: [AMBER] strip and use of distance-based mask
Hi,
I am able to successfully run using the topology and restart you
provided with input:
trajin mdrest.1
reference mdrest.1
strip !(:1-107<.6.0)
trajout 1.pdb pdb
go
However, I do see some strange memory access behavior in the AT1.2
version of ptraj that I don't see in the AT1.5 version, so it's
probably best you upgrade.
-Dan
On Wed, Feb 29, 2012 at 11:32 AM, Nanna Holmgaard List
<nalis07.student.sdu.dk> wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 29 2012 - 13:00:03 PST
