Anna Marabotti wrote:
Dear Luca, dear all,
thank you for your hints. I made some trials with my systems and these are
my answers to your questions:
- my system is a protein (with or w/o ligand) in solvent (water SPC).
Following your suggestions, I tried to perform an EM on the protein w/o
ligand after the editconf step (i.e. I created the topology with pdb2gmx,
created a cubic box with editconf, then I used grompp+mdrun to perform EM).
I received the same error: the minimization starts, performs 37 steps, then
stops with the "stepsize too small...." communication. The energy in this
case is -3.06e+4 (one order of magnitude higher than the solvated system)
but still negative, and the maximum force is still "inf on atom 1". So
minimizing in vacuo does not help to solve the problem. This atom 1 is the
Nter of the protein, it is belonging to a Ser and I did not charge it
explicitly with pdb2gmx (i.e. I did not use the flag -ter) but it is bound
to 3 H in the .gro file.
Were there any messages from pdb2gmx when you produced your topology? How large
is your box? What force field are you using?
- If I look at the protein with VMD or other visualizing tools, it seems to
me that no major problems are present on the structure. In particular, atom
1 is not "broken" or something similar, I can't see no "aberrations". I
don't know how to check if something goes wrong apart from visualization, do
you know some tools that could automatically check the file? To the best of
my knowledge, gmxcheck performs checks only on trajectories, or can I use it
also on single structures?
There is no tool for troubleshooting this kind of problem. gmxcheck will
inspect the integrity of a file (including single structures), but will not
magically tell you what's wrong with it :)
- I also tried to continue anyway after the minimization step with the PR MD
in NVT, but it did not start because of a lot of LINCS error. It suggests me
that some distortions are present in my structure, but if I cannot minimize
it, how to relieve this problem?
If a system does not minimize, any further steps will be futile.
<snip>
G96Bond G96Angle Proper Dih. Improper Dih. LJ-14
2.40716e+03 1.23569e+03 6.85831e+02 8.70819e+01 2.11992e-314
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip.
2.11992e-314 -2.19860e+03 -1.52663e+02 -6.70307e+03 -2.59368e+04
Potential Pressure (bar)
-3.05754e+04 nan
The fact that your LJ-14 and Coulomb-14 energies are essentially numerical
infinity (!) suggests some very bad underlying problem. Hard to say at this
point what it is though.
Other useful information would be the actual .mdp file you're using, and answers
to my questions above.
-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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