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
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