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

[Justin A. Lemkul]

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

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

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

========================================