From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Tue Jul 05 2011 - 10:34:16 CDT
Dear Rajan,
Thanks a lot for the hint, it worked perfectly!
FYI I used the following command
$vmd -dispdev text -eofexit < input.tcl > output.log
and (always FYI) my input.tcl script is the following:
#######################################
# tcl script to convert NAMD binary
# coordinates file (.coor) into pdb file.
mol new top.prm type parm7 first 0 last -1 step 1 filebonds 1
autobonds 1 waitfor all
mol addfile min.1.coor type namdbin first 0 last -1 step 1 filebonds 1
autobonds 1 waitfor all
set sel [atomselect top all]
$sel writepdb min.1.pdb
#######################################
Cheers!
MP
2011/7/2 Rajan Vatassery <rajan_at_umn.edu>:
> Dear Massimiliano,
> Check out this thread on the subject of the .coor files:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13295.html
>
> It contains 2 possible solutions that you may find useful. I know that
> the python script included in this thread works well and it's fairly
> short (hopefully that translates into ease of understanding).
>
> Best of luck,
>
> rajan
>
>
> On Sat, 2011-07-02 at 19:21 +0100, Massimiliano Porrini wrote:
>> Dear all,
>>
>> I have generated 500 NAMD coordinates files which have the
>> following type of name:
>>
>> min.N.coor
>>
>> where N=1,...,500 .
>>
>> and in the runs I used Amber force field parameter file.
>>
>> I would like to convert them into PDB file format.
>>
>> Can anybody give me a hint on which is an efficient way to do that?
>>
>> Thank you in advance.
>>
>> Best regards,
>> MP
>>
>>
>>
>
>
>
-- Dr Massimiliano Porrini Institute for Condensed Matter and Complex Systems School of Physics & Astronomy The University of Edinburgh James Clerk Maxwell Building The King's Buildings Mayfield Road Edinburgh EH9 3JZ Tel +44-(0)131-650-5229 E-mails : M.Porrini_at_ed.ac.uk mozz76_at_gmail.com maxp_at_iesl.forth.gr
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