Thomas, when I use ptraj to extract frames from a trajectory, using the
restart format, I don't have the problem you do. My frames have the correct
box info at the end of the rst files.
Do you have the right box information in the parameter file (look under
%FLAG BOX_DIMENSIONS)? I know that the info in the restart file is the
important one, but maybe in ptraj, for some reason, the info in the
parameter file is also important?
I hope this helps,
Ignacio
On Thu, Mar 24, 2011 at 1:10 PM, <thomas.fox.boehringer-ingelheim.com>wrote:
> Hi,
>
> I have a system with a truncated octahedron as my solvent box.
> Accordingly,
> the last line of my restart file reads something like
> 27.141 27.141, 27.141 109.471... 109.471... 109.471
>
> Now I noticed that when I use ptraj (Ambertools 1.4), the information that
> it
> is a octahedral box seems to get lost when I use the commands
> trajin input.crd
> trajout output.crd restart
>
> Then my last line in the generated restart file only has the x, y, z
> dimensions of the box, but not the angles.
>
> 1) is this a problem? I would guess yes, as - if I understood the
> documentation correctly - the box dimensions are taken exclusively from the
> restart file.
> 2) I guess I could use the box command in ptraj to fix this - but I'd
> rather have the box information (size *plus* shape) carried over to the
> output file automatically. Is there an easy way to do this?
>
> Thanks,
> Th.
>
> Mit freundlichen Grüßen / Kind regards,
> Dr. Thomas Fox
>
> Boehringer Ingelheim Pharma GmbH & Co. KG
> Lead Identification and Optimization Sup
> Tel.: +49 (7351) 54-7585
> Fax: +49 (7351) 83-7585
> mailto:thomas.fox.boehringer-ingelheim.com
>
> Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
> Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
> Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
> Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
> des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
> Registergericht Mainz: HR B 23260
>
> Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen
> Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie
> bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail
> und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte
> Bearbeitung,
> Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is
> confidential and may also be legally privileged. If you are not the
> intended
> recipient please reply to sender, delete the e-mail and do not disclose its
> contents to any person. Any unauthorized review, use, disclosure, copying
> or
> distribution is strictly prohibited.
>
>
> _______________________________________________
> 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 Thu Mar 24 2011 - 10:30:05 PDT
