VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Sep 22 2014 - 18:07:48 CDT

Hi,

I have data in DCD trajectories. I need to use something in the gromacs
package, one way of which is to convert dcd to xtc/trr.

I use -

catdcd.exe -o ala.xtc -dcd alanin.dcd

which gives this:

CatDCD 5.2
dcdplugin) detected standard 32-bit DCD file of opposite endianness
dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
Opening file 'ala.trr' for writing.
dcdplugin) detected standard 32-bit DCD file of opposite endianness
dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)
Opened file 'alanin.dcd' for reading.
Read 100 frames from file alanin.dcd, wrote 100.
Total frames: 100
Frames written: 100
CatDCD exited normally.

alanin.dcd is a 66 atom 100 frame trajectory in the VMD install, which I am
using to test the system.

ala.xtc is then visualized using VMD which is where the problem emerges (if
it is a problem).

In the VMD install there is a alanin.pdb holding 66 atoms. That is loaded
into VMD and ontop of that I try to load the xtc file that I just made.

Error: Unable to load molecule (in the vmd gui)

at the backend in the command line the shell is showing:

gromacsplugin) Cannot read header from '(file path).xtc', no error
ERROR) Couldn't read file (same path as above)

Question: Did CatDCD mess up - or is it the way I am loading the structure.
Question: A missing header means (usually) trajectory wasn't made
correctly. Right ?
Question: If I pass both (pdb/xtc) of these files to Gromacs, and it by
chance works, is the system trustable ?

My system specs are 32-Bit windows running CatDCD 32-bit 5.2.

Any help would be appreciated.

Best,
/A 

-- 
Best,
/A