Andrew Voronkov wrote:
Dear GROMACS users,
I'm trying to do this tutorial
It's always best to post a link to the tutorial you're using. There are dozens
of Gromacs tutorials out there.
with 1ijy structure from rcsb.org
All .gro files on different step raise questions.
1) conf.gro - by VMD I see some strange groups which are not linked with the
protein.
This may or may not be an artefact of VMD's efforts to guess where bonds should
be. Sometimes it's smart, sometimes it's not.
2) After solvatation step in solvated.gro the protein is not in the middle of
solution but somewhere in the edge, how to solve this?
editconf -c
3) After energy minimization protein even goes out of the solution. Looks like
I am doing everything according to the tutorial (except the structure) but
there are still problems...
Use editconf -c and try again.
The .gro files are in the attachment.
The listserv ate them, but they probably won't aid much in diagnosis, anyway.
On minimization step I also get:
Steepest Descents converged to machine precision in 73 steps,
but did not reach the requested Fmax
Depending on what your target Fmax was, this may not be a problem. Fmax < 1000
is generally adequate for a simple protein in water.
On equilibration step I also get an error(with such .gro file it very
proabable):
Or you could have an error in your .mdp file (inappropriate parameters, etc), so
if things continue to fail, post the .mdp file (not as an attachment, just embed
the text).
-Justin
Warning: 1-4 interaction between 2 and 19 at distance 2.795 which is larger
than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
t = 0.000 ps: Water molecule starting at atom 33175 can not be settled.
Check for bad contacts and/or reduce the timestep.
Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
Best regards,
Andrew
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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