Re: a bundle of coor files

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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