NAMD Wiki: NamdAndXPLOR
A crystallography program using the CHARMM force field, see http://xplor.csb.yale.edu/xplor/
Why is the timestep incorrect in DCD files?
I assume you are using X-PLOR to read the trajectories. A couple of years ago, after X-PLOR development stopped, the NAMD DCD format was adjusted slightly to conform to the CHARMM specification. The difference between the two is that while X-PLOR used a double for the timestep, CHARMM uses the same space for a float followed by an int. That int is important because it indicates if the file contains data about the periodic cell, a recent addition. It was previously ignored so CHARMM and X-PLOR could exchange DCD files with only a bad timestep, but now CHARMM rejects X-PLOR written files unless the timestep is zero.
I would suggest trying to cope with the incorrect timestep. If you can't the NAMD source distribution contains dumpdcd.c and loaddcd.c, which can be used to set the headers to whatever you want, and fixdcd.c, which can be modified to fix your problem (it currently changes X-PLOR to CHARMM).
Why does NAMD complain about missing vdw parameters?
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE 0.000000E+00
If you don't specify a segment name, the second column in the psf file will be blank and NAMD will misread the charge as the atom type. Fix this by adding name="MAIN" to your segment statement in X-PLOR or giving the segname as the first argument to GENErate in CHARMM.
Why does NAMD complain about CHARMM format?
FATAL ERROR: Structure (psf) file is in CHARMM format; XPLOR format required.
CHARMM can create psf files in either CHARMM format (which uses numbers for atom types) or X-PLOR format (which uses names for atom types). NAMD uses X-PLOR format both for historical reasons, and because it is more robust. If NAMD sees a numerical atom type it tries to be helpful with this message. The solution is to use "write psf card xplor" when creating the PSF file.
If you did this (or used X-PLOR in the first place) then you probably have a blank segment name. If you don't specify one, the second column in the psf file will be blank and NAMD will misread the charge as the atom type. Fix this by adding name="MAIN" to your segment statement in X-PLOR or giving the segname as the first argument to GENErate in CHARMM.