VMD-L Mailing List

From: R. Charbel Maroun (charbel.maroun_at_inserm.fr)
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
viceversa;
     - NAMD takes as input coordinates only pdb format files.

Cheers,

CMaroun

Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> 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:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node207.html
>
> You could also consider using catDCD for this.
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> 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
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node13.html#SECTION00062200000000000000
>
> Regards,
> Ajasja
>

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