Re: saving coordinates as a PDB file after minimization in NAMD

From: LEWYN LI (
Date: Tue Oct 25 2005 - 16:32:19 CDT


         You could just start the simulation with the binary .coor file.
If you wish to do that, you need to specify BOTH "coordinates" and
"bincoordinates" in your .conf file. For example:

coordinates something.pdb
bincoordinates the_coor_file_from_minimization.coor

         The coordinates in "something.pdb" will be ignored.

         If you absolutely do not want to use binary .coor, you can load
the binary .coor into vmd (you need to invoke the .psf file first) and
then save the coordinates as pdb via "File -> Save coordinates". You lose
a little bit of accuracy with ASCII relative to binary.

         Hope this helps.


On Tue, 25 Oct 2005, Richard Law wrote:

> If your .coor is in binary then you have binaryoutput set to "yes". You need
> to change that. (to "no".)
> Rich.
> On Tue, 25 Oct 2005, Richard Wood wrote:
>> Hi all,
>> How does on save the resulting coordinates of a NAMD
>> minimization in a format to do dynamics?
>> I have a starting PDB and I want to run 1000 steps of
>> minimization, save it to a second PDB file and then
>> run dynamics.
>> It says in the NAMD manual to use:
>> "outputname < output PDB file >
>> Acceptable Values: UNIX filename prefix
>> Description: At the end of every simulation, NAMD
>> writes two PDB files, one containing
>> the final coordinates and another containing the final
>> velocities of all atoms in the simulation.
>> This option specifies the file prefix for these two
>> files. The position coordinates will be saved
>> to a file named as this prefix with .coor appended.
>> The velocities will be saved to a file named
>> as this prefix with .vel appended. For example, if the
>> prefix specified using this option was
>> /tmp/output, then the two files would be
>> /tmp/output.coor and /tmp/output.vel."
>> However, .coor files are binary files.
>> So how do I obtain the coordinates?
>> Richard
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