AMBER Archive (2006)

Subject: AMBER: Trimming ptraj output

From: Andy Purkiss (
Date: Fri Jan 13 2006 - 11:29:00 CST

Dear Amberers,

I'm switching over to use ptraj from carnal. Carnal has an option in the
FILES_OUT section allowing the user to only output every n snapshots:

COORD crd ./nowat.crd CRD MOD n;

Is there a way to do this with ptraj, other than by altering the trajin
lines? I don't want to do this as this will affect the analysis of rmsd

Also, a question to the author. Is it possible to stop ptraj checking
all the input files at the beginning of the run. My trajin files are
compressed and ptraj appears to run though the files before starting the
analysis and then again when all the input has been read actually
performing the analysis. This leads to a considerable pause before
analysis actually starts.

Maybe just a simple check that the file exists would be possible rather
than a complete run though as this didn't catch my mistake with
mismatched parameter and trajectory files!!

Andy Purkiss

Cat, n.: Lapwarmer with built-in buzzer.
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail                   |

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to