NAMD to CHARMM unit cell information in DCD

From: François Marchand (fmarchand_at_bioc.unizh.ch)
Date: Tue Oct 30 2007 - 14:29:41 CDT

Dear All,

I simulated several systems with NAMD-2.5 (CPT conditions) and I want to
analyze the trajectories with CHARMM, and specifically I would like to reset
the correct cell dimensions.

The problem is that I forgot to set the 'DCDUnitCell' option to 'yes', and
according to
( http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4990.html )
the default option in NAMD-2.5 is 'no'.

My question is: are the cell informations coded somewhere in the NAMD-dcd's or
are they definitively lost (what I expect...)?

If yes, how can I recover them in CHARMM format?

I tried 'catdcd' and
'dcdcellfix' (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2617.html)
(they set the cell dimension to 1.00 for every frame) and numerous CHARMM
scripts, but always unsuccessful thus far!

Thanks in advance for an answer!

                François

-- 
________________________________________________
François Marchand
Department of Biochemistry, Caflisch Group
University of Zurich, Winterthurerstrasse 190
CH-8057 Zuerich / Switzerland
 
 Phone  +41 1 635 55 59
 Fax      +41 1 635 68 62

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