AMBER Archive (2008)

Subject: Re: AMBER: Ptraj / ambmask | Using distance-based masks to strip a trajectory

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Jun 11 2008 - 10:55:12 CDT

Hi, Ian,

Since the parsing of mask is done before reading the actual frames, the
ptraj requires a structure as reference for the atom coordinates. As you may
imagine, the selection is static. To emphasize this, the distance-based mask
selection requires an explicit structure using "reference" command. For this
reason, the "checkmask" command or other commands in rdparm will not be able
to check the distance-based mask selection.

Please try the following script:

trajin test.trj
reference test.trj
strip "(:1 >@5.0)"
trajout strip1.trj nobox

Also pay attention to the output of ptraj. It will print out the mask
selection for each command. Please check them if you have any suspicion.

Best,

Jianyin Shao

On 6/11/08, Ian <ian2craig_at_gmail.com> wrote:
>
> Thanks Vlad and David for that advice, but I've still not been able to use
> ptraj to strip away atoms based on their distance from some reference atom
> or residue.
>
> To illustrate my problem, I've taken a single frame from a protein MD
> simulation (using ptraj) and put it in a file called test.trj (Amber
> trajectory format). I then try the following two ptraj operations:
>
> trajin test.trj
> strip "(:1 >@5.0)"
> trajout strip1.trj nobox
>
> trajin test.trj
> strip "(:1 <@5.0)"
> trajout strip2.trj nobox
>
> Note that the first tries to strip all atoms further than 5 Angstroms from
> the first residue, and the second tries to strip all atoms closer than 5
> Angstroms to the first residue.
>
> As described in the original post, the ptraj that comes with Amber9 just
> freezes. The most recent ptraj (version 9.9h) executes -- but strip1.trj and
> strip2.trj are identical! This is clearly not the result I expected. The
> ptraj that comes with AmberTools throws a segmentation fault.
>
> I've read the manual and tried to search the mailing list archive. I can't
> figure out what I'm doing wrong here -- if you can see it, please point it
> out, however obvious. I'd be very grateful. I'd also like to know if this
> functionality is known to be .. not functioning.
>
> Many thanks,
>
> Ian.
>
>
> On Fri, Jun 6, 2008 at 7:50 PM, Vlad Cojocaru <
> Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>
>> Sorry, of course. While writing the answer I shortly forgot about it.
>> AmberTools is for free so the latest ptraj is to be found there.
>>
>> vlad
>>
>>
>>
>> David Case wrote:
>>
>> On Fri, Jun 06, 2008, Vlad Cojocaru wrote:
>>
>> I believe the ptraj from AMBER9 does not implement the new mask parser
>> (I believe this type of mask is available only in the new parser). What
>> I would suggest if you dont have AMBER10 is to download the stand-alone
>> version of ptraj from Tom Cheatham's webpage (latest version is 9.9h I
>> believe).
>>
>> Please note that ptraj is a part of the (free) AmberTools package, not
>> Amber10. To get the lastest version of ptraj, you should download and install
>> AmberTools from http://ambermd.org.
>>
>> ...dac
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>>
>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu