On 4/23/12 11:01 AM, Lara Bunte wrote:
Hi

What do you mean with


Specify a .pdb file as the output of your original command.

I wrote in


trjconv -s -f output.xtc -o output.pdb


in the last part output.pdb. What should I specify more?


When I was referring to your "original command," I meant this one:

trjconv -n index.ndx -f my_molecule.pdb -o output

At this point, trjconv expects that you want an .xtc (trajectory) file, since you did not explicitly specify an extension. An .xtc file contains no information regarding atom names, so converting it back to a .pdb file requires a .tpr file, as the error you got (below) indicates. If you want to make your life simple, be more specific in what you tell trjconv. Want a .pdb file? Tell it so:

trjconv -n index.ndx -f my_molecule.pdb -o output.pdb

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Reply via email to