VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Aug 19 2010 - 16:19:10 CDT

I just downloaded the latest version of standalone catdcd. I don't want to use the VMD plugin because I don't have enough memory for the whole trajectory. I want to extract the C-alphas from chain A only & created an index file for it.
 
I entered:
 ~/catdcd -o HGbIAcAca10th.dcd -otype dcd -i HGbIAcAca.idx -stype pdb -s v4fe3ac-all.pdb -dtr clickme.dtr

I put the .idx file .pdb files in the same dir as clickme.dtr. The pdb file contains the entire structure, not just chain A C-alphas.
 
I get this message:
CatDCD 4.0
Reading indices from file 'HGbIAcAca.idx'
Opening file 'HGbIAcAca10th.dcd' for writing.
Could not find timekeys file at /timekeys
Error: could not open file 'clickme.dtr' for reading.

I *do* have a timekeys file, but it's in the same dir as clickme.dtr, not in its own dir. It's also called timekeys... So I just tried creating a timekeys dir & moved timekeys into it. Still got the same message. Where should /timekeys be so this will work? [Yes, it's a bandaid, but I'm all for what works fastest].
 
Thanks!
Irene Newhouse