X Rules wrote:
>
> There was a bug in an early 4.0.x feature that box vectors were not
properly
> written to .pdb files (CRYST line), but this was obviously fixed
months, if not
> a year or more, ago. Gromacs tools are expected to handle numerous
file types
> effortlessly, so using .gro is certainly not required. If you have
direct
> evidence that some tool has written or interpreted the box
incorrectly, then
> please file a bugzilla, but otherwise something else likely went wrong.
>
> -Justin
well I will check a bit more and submit it to bugzila as there is no
cryst line if you write a pdb with genion .. so that might be the root
cause to my problems.
I would investigate that very thoroughly and be very sure it's reproducible
before submitting a bugzilla. I've run through an entire workflow (pdb2gmx,
editconf, genbox, genion, grompp, mdrun) with lysozyme using both .gro and .pdb
files and everything works fine either way. That doesn't preclude the
possibility of a bug somewhere, but I would think it very unlikely that a bug
exists in something so fundamental that was fixed a very long time ago.
-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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