From: R. Charbel Maroun (
Date: Fri Feb 10 2012 - 09:25:21 CST

Hi VMDers,

Thanks to all for having taking the time to reply to the two (silly)
questions I asked. Conclusions :
     - can't write both, binary (coor) and ascii (pdb) coordinate
files with NAMD. Have to go through VMD or other for coor => pdb or
     - NAMD takes as input coordinates only pdb format files.



Ajasja Ljubetič <> a écrit :

>> Is it possible to run VMD in stand-alone (non-graphical) mode ? Within a
>> script, I just want to be able to read a .coor NAMD binary file and save it
>> as an ASCII
>> .pdb file for further use in NAMD.
>> Indeed it's possible:
> use vmd -dispdev text -e "path to script to load and save your stuff"
> More info here:
> You could also consider using catDCD for this.
> An alternative question is, how can I get NAMD to write a .pdb file
>> after an MD ? I tried writepdb <filename> in an NAMD script and it gives
>> the following error:
> Try *binaryoutput no*
> More info here
> Regards,
> Ajasja

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