AMBER Archive (2009)

Subject: [AMBER] ptraj and namd charmm dcd

From: Sandro L. Fornili (
Date: Wed Apr 01 2009 - 10:59:37 CDT

Dear Amber Users,

I would like to use ptraj (AmberTools-1.2) to analyse dcd trajectories
produced by NAMD with CHARMm ff. I can transform dcd to restart format
but I am not able to center a tripeptide solute within its water box.
For the simulation I used the the psf file in X-PLOR format as required
by NAMD, while with ptraj I use the same file in the CHARMm format, both
obtained from the VMD-1.8.6 AutoPSF. Is this the expected behaviour of
ptraj or there something wrong in the attached small case?

Thank you in advance for your help


Sandro L. Fornili
Dipartimento di Tecnologie dell'Informazione
Universit` degli Studi di Milano
Via Bramante 65, 26013 Crema (CR), Italy

Tel. +39 02-503-30067 Fax +39 02-503-30010

  • application/octet-stream attachment: trj.tgz

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