[gmx-users] File editing - only one layer of water around a molecule

Lara Bunte lara.bunte at yahoo.de
Mon Apr 30 17:41:27 CEST 2012


I have the command 

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

that don't work because of the missing topol.tpr file. You wrote:

>Supply your .pdb file to the -s flag

Where exactly do I have to write -s in my command? 

Thanks for help


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 19:44 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule

On 4/23/12 1:27 PM, Lara Bunte wrote:
> Hi
> In this case my problem is not solvable with gromacs?
> All I have is the my_molecule.pdb which is a small molecule in a water box and my generated index.ndx file, size.xvg file and output.xtc file.

Supply your .pdb file to the -s flag.  Sorry for my confusion.  If your desired output requires atom names, etc. you must invoke -s to read those names.  An .xtc file is agnostic to all this information.  Thus in your case, you need a source of atom/residue naming.  A .tpr file is not strictly required for this purpose, but again, be mindful of what Gromacs expects as default input - that is why the error is coming up.  Under most circumstances for trjconv operations, a .tpr file is passed to -s, but in your case, a .pdb will suffice.


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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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