[gmx-users] File editing - only one layer of water around a molecule
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:
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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