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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 23 19:44:32 CEST 2012

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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