- 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?
The choice of FF and different outcome of GMX could address the problem
in more precise way.
And yes, does pdb2gmx plainly goes till the end of topology generation ?
Moreover, did you try a larger box, even at great extent with respect to
protein ?
Are there any warning during the "grompping" step ? A mismatch of atoms
in principle could lead to such errors at the beginning of calculations.
- 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?
VMD could not necesserely tell the truth ... :).
It could be not a problem of visualization.
- 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.
Minimization looks for a local minimum: maybe some troubles in LINCS
derive from some problems related to uncorrect distributions of dihedral
angles or sidechain stereochemistry that
a steepest descent could not properly correct. In such a case, I guess
Modeller (or whatever) could have generated a structure that is really
far away from local minima.
Of course, the correct procedure is a. minimization b. positional
restrained MD c. production run : however, you could try a workaround of
the problem setting up a short low temperature
simulation of the protein as-it-is in vacuo (few ps at few K degrees,
for example) and see what happens. In this way you are forcing the
protein to get in action but with variations that could not (in principle)
result in a so verbose output of LINCS (i.e., it could result in a
system that does not violate very much the LINCS "rules"). If the thing
goes fine, it will not be the cleanest way to proced, however you could
argue which the problem could be, try to fix it and go back to and
through the standard procedure.
It's a "dirty" suggestion, I know, but at this point it's worth to try ...
<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.
Yes, the mdp file at this point is essential, even if the preciously
attached text should include all the things used and required for better
understanding.
Cheers.
Luca
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