Dear Amber users,
I wanted to add a point that when I create the topology and coordinate files for
the protein-ligand-trna complex dimer, the following is the output:
153 Na+ ions required to neutralize.
Adding 153 counter ions to "3zni" using 1A grid
Grid extends from solute vdw + 1.87 to 7.97
Resolution: 1.00 Angstrom.
grid build: 2 sec
(no solvent present)
Calculating grid charges
charges: 280 sec
Placed Na+ in 3zni at (-32.72, 27.71, 34.76).
Placed Na+ in 3zni at (-25.72, 31.71, -33.24).
Placed Na+ in 3zni at (-19.72, 28.71, 35.76).
Placed Na+ in 3zni at (-33.72, 29.71, -35.24).
Placed Na+ in 3zni at (-30.72, 36.71, 34.76).
Placed Na+ in 3zni at (-6.72, 15.71, 40.76).
Placed Na+ in 3zni at (-20.72, 34.71, -35.24).
Placed Na+ in 3zni at (-21.72, 18.71, -34.24).
Placed Na+ in 3zni at (-32.72, 23.71, 36.76).
Placed Na+ in 3zni at (-21.72, 35.71, 43.76).
Placed Na+ in 3zni at (-13.72, 17.71, 46.76).
Placed Na+ in 3zni at (-26.72, 15.71, -42.24).
Placed Na+ in 3zni at (-34.72, 42.71, 39.76).
Placed Na+ in 3zni at (-13.72, 16.71, -47.24).
Placed Na+ in 3zni at (-34.72, 23.71, -35.24).
Placed Na+ in 3zni at (-39.72, 28.71, 30.76).
Placed Na+ in 3zni at (5.28, 20.71, 47.76).
Placed Na+ in 3zni at (-27.72, 37.71, -31.24).
Placed Na+ in 3zni at (-17.72, 26.71, 48.76).
Placed Na+ in 3zni at (-25.72, 40.71, -21.24).
Placed Na+ in 3zni at (-38.72, 30.71, -38.24).
Placed Na+ in 3zni at (-5.72, -5.29, -44.24).
Placed Na+ in 3zni at (-1.72, 18.71, 44.76).
Placed Na+ in 3zni at (-24.72, 39.71, 35.76).
Placed Na+ in 3zni at (-27.72, 17.71, -31.24).
Placed Na+ in 3zni at (-39.72, 26.71, 21.76).
Placed Na+ in 3zni at (-8.72, 11.71, -39.24).
Placed Na+ in 3zni at (-2.72, 20.71, 37.76).
Placed Na+ in 3zni at (-33.72, 32.71, 29.76).
Placed Na+ in 3zni at (-10.72, 1.71, -37.24).
Placed Na+ in 3zni at (-21.72, 35.71, -39.24).
Placed Na+ in 3zni at (-35.72, 1.71, 5.76).
Placed Na+ in 3zni at (-19.72, 13.71, -48.24).
Placed Na+ in 3zni at (-14.72, 20.71, 52.76).
Placed Na+ in 3zni at (-6.72, 15.71, -46.24).
Placed Na+ in 3zni at (-17.72, 33.71, 45.76).
Placed Na+ in 3zni at (-31.72, 38.71, -24.24).
Placed Na+ in 3zni at (-30.72, 21.71, -42.24).
Placed Na+ in 3zni at (7.28, 16.71, 54.76).
Placed Na+ in 3zni at (-35.72, 27.71, 15.76).
Placed Na+ in 3zni at (-13.72, 7.71, -29.24).
Placed Na+ in 3zni at (-12.72, 12.71, 41.76).
Placed Na+ in 3zni at (-6.72, 41.71, -14.24).
Placed Na+ in 3zni at (-29.72, 31.71, 33.76).
Placed Na+ in 3zni at (-7.72, 23.71, 32.76).
Placed Na+ in 3zni at (-22.72, 23.71, -35.24).
Placed Na+ in 3zni at (-30.72, 45.71, 34.76).
Placed Na+ in 3zni at (-34.72, 7.71, 14.76).
Placed Na+ in 3zni at (-42.72, 33.71, 21.76).
Placed Na+ in 3zni at (-45.72, 35.71, -41.24).
Placed Na+ in 3zni at (-39.72, 27.71, 42.76).
Placed Na+ in 3zni at (-45.72, 44.71, 46.76).
Placed Na+ in 3zni at (-3.72, 4.71, -39.24).
Placed Na+ in 3zni at (-26.72, 37.71, -43.24).
Placed Na+ in 3zni at (-14.72, 29.71, 51.76).
Placed Na+ in 3zni at (-8.72, 44.71, -0.24).
Placed Na+ in 3zni at (-31.72, 14.71, -36.24).
Placed Na+ in 3zni at (-16.72, 38.71, 37.76).
Placed Na+ in 3zni at (-4.72, -6.29, -48.24).
Placed Na+ in 3zni at (-29.72, 32.71, -29.24).
Placed Na+ in 3zni at (4.28, 22.71, 43.76).
Placed Na+ in 3zni at (-11.72, 14.71, -51.24).
Placed Na+ in 3zni at (-15.72, 16.71, -56.24).
Placed Na+ in 3zni at (-43.72, 25.71, -34.24).
Placed Na+ in 3zni at (-39.72, 7.71, 4.76).
Placed Na+ in 3zni at (-34.72, 45.71, 44.76).
Placed Na+ in 3zni at (-28.72, 42.71, -17.24).
Placed Na+ in 3zni at (-19.72, 37.71, 26.76).
Placed Na+ in 3zni at (-12.72, -5.29, -40.24).
Placed Na+ in 3zni at (-27.72, 35.71, 47.76).
Placed Na+ in 3zni at (-0.72, 43.71, -3.24).
Placed Na+ in 3zni at (-3.72, 27.71, 28.76).
Placed Na+ in 3zni at (-1.72, 12.71, -39.24).
Placed Na+ in 3zni at (-40.72, 28.71, -44.24).
Placed Na+ in 3zni at (-18.72, 29.71, -15.24).
Placed Na+ in 3zni at (-31.72, 44.71, -27.24).
Placed Na+ in 3zni at (-23.72, 27.71, 36.76).
Placed Na+ in 3zni at (-23.72, 32.71, -50.24).
Placed Na+ in 3zni at (-34.72, 19.71, -27.24).
Placed Na+ in 3zni at (-41.72, 30.71, 26.76).
Placed Na+ in 3zni at (7.28, 12.71, 57.76).
Placed Na+ in 3zni at (-39.72, 15.71, 4.76).
Placed Na+ in 3zni at (-41.72, 48.71, 39.76).
Placed Na+ in 3zni at (-34.72, -5.29, 9.76).
Placed Na+ in 3zni at (-13.72, 1.71, -28.24).
Placed Na+ in 3zni at (-37.72, 19.71, 42.76).
Placed Na+ in 3zni at (-40.72, 41.71, -49.24).
Placed Na+ in 3zni at (0.28, 17.71, 32.76).
Placed Na+ in 3zni at (-28.72, -2.29, 28.76).
Placed Na+ in 3zni at (-23.72, 29.71, 52.76).
Placed Na+ in 3zni at (-27.72, 11.71, -45.24).
Placed Na+ in 3zni at (-24.72, 21.71, 15.76).
Placed Na+ in 3zni at (1.28, 13.71, -48.24).
Placed Na+ in 3zni at (-23.72, 42.71, -29.24).
Placed Na+ in 3zni at (-28.72, 49.71, 6.76).
Placed Na+ in 3zni at (-24.72, 7.71, -26.24).
Placed Na+ in 3zni at (6.28, -2.29, -51.24).
Placed Na+ in 3zni at (-6.72, 45.71, -10.24).
Placed Na+ in 3zni at (-14.72, 21.71, 44.76).
Placed Na+ in 3zni at (-44.72, 28.71, 17.76).
Placed Na+ in 3zni at (4.28, 38.71, -23.24).
Placed Na+ in 3zni at (-7.72, 8.71, -33.24).
Placed Na+ in 3zni at (7.28, 23.71, 50.76).
Placed Na+ in 3zni at (-33.72, 9.71, -2.24).
Placed Na+ in 3zni at (-33.72, 38.71, 36.76).
Placed Na+ in 3zni at (-14.72, 34.71, -44.24).
Placed Na+ in 3zni at (-27.72, 22.71, -26.24).
Placed Na+ in 3zni at (-11.72, 37.71, 46.76).
Placed Na+ in 3zni at (-39.72, 29.71, 50.76).
Placed Na+ in 3zni at (-26.72, 23.71, -55.24).
Placed Na+ in 3zni at (-38.72, 25.71, 35.76).
Placed Na+ in 3zni at (2.28, 25.71, 38.76).
Placed Na+ in 3zni at (-1.72, -8.29, -39.24).
Placed Na+ in 3zni at (-16.72, -10.29, -7.24).
Placed Na+ in 3zni at (-7.72, 41.71, 3.76).
Placed Na+ in 3zni at (-29.72, 4.71, 24.76).
Placed Na+ in 3zni at (-19.72, 17.71, -44.24).
Placed Na+ in 3zni at (-14.72, 31.71, 33.76).
Placed Na+ in 3zni at (-14.72, 13.71, 49.76).
Placed Na+ in 3zni at (-15.72, 11.71, 52.76).
Placed Na+ in 3zni at (8.28, 44.71, -7.24).
Placed Na+ in 3zni at (-23.72, 36.71, -16.24).
Placed Na+ in 3zni at (4.28, 48.71, 12.76).
Placed Na+ in 3zni at (-43.72, 13.71, -7.24).
Placed Na+ in 3zni at (-29.72, 48.71, 27.76).
Placed Na+ in 3zni at (-44.72, 41.71, -43.24).
Placed Na+ in 3zni at (2.28, 13.71, 59.76).
Placed Na+ in 3zni at (0.28, 21.71, -17.24).
Placed Na+ in 3zni at (3.28, 5.71, -50.24).
Placed Na+ in 3zni at (-13.72, 26.71, 56.76).
Placed Na+ in 3zni at (-9.72, 26.71, 62.76).
Placed Na+ in 3zni at (-7.72, 23.71, 59.76).
Placed Na+ in 3zni at (-32.72, -10.29, -14.24).
Placed Na+ in 3zni at (-36.72, 33.71, 20.76).
Placed Na+ in 3zni at (-9.72, 15.71, 1.76).
Placed Na+ in 3zni at (-36.72, 36.71, -17.24).
Placed Na+ in 3zni at (-4.72, 18.71, -38.24).
Placed Na+ in 3zni at (9.28, 38.71, 24.76).
Placed Na+ in 3zni at (-34.72, 38.71, -50.24).
Placed Na+ in 3zni at (-47.72, 37.71, 43.76).
Placed Na+ in 3zni at (-43.72, 32.71, 44.76).
Placed Na+ in 3zni at (-39.72, 5.71, 10.76).
Placed Na+ in 3zni at (-0.72, 0.71, -33.24).
Placed Na+ in 3zni at (12.28, 21.71, 4.76).
Placed Na+ in 3zni at (-11.72, 48.71, -6.24).
Placed Na+ in 3zni at (-45.72, 28.71, -10.24).
Placed Na+ in 3zni at (-27.72, 36.71, 55.76).
Placed Na+ in 3zni at (-4.72, -5.29, -54.24).
Placed Na+ in 3zni at (-26.72, 6.71, -39.24).
Placed Na+ in 3zni at (-15.72, 42.71, 25.76).
Placed Na+ in 3zni at (-34.72, -3.29, 17.76).
Placed Na+ in 3zni at (-45.72, 30.71, -37.24).
Placed Na+ in 3zni at (14.28, 36.71, 8.76).
Done adding ions.
Solute vdw bounding box: 65.736 70.536 122.736
Total bounding box for atom centers: 93.736 98.536 150.736
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 96.499 101.406 154.021 angstroms.
Volume: 1507176.014 A^3
Total mass 800392.986 amu, Density 0.882 g/cc
Added 38029 residues.
Checking Unit.
WARNING: There is a bond of 30.500389 angstroms between:
------- .R<RA3 712>.A<N7 16> and .R<RA3 712>.A<C5 17>
WARNING: There is a bond of 31.529394 angstroms between:
------- .R<RA3 712>.A<C8 14> and .R<RA3 712>.A<N7 16>
WARNING: The unperturbed charge of the unit: -0.999880 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<YLY 361>: C3 N4 C5 N5
<YLY 361>: C1 C5 C3 N2
<YLY 361>: H4 N1 C2 N2
<YLY 361>: C5 H1 N5 H2
<YLY 361>: H3 N3 C4 N4
<YLY 361>: C3 N1 C1 N3
<YLY 361>: C6 C1 N1 C2
<YLY 361>: C12 O8 C11 O3
<YLY 361>: C18 N7 C17 O9
<YLY 361>: C20 H31 C19 N8
<YLY 713>: C3 N4 C5 N5
<YLY 713>: C1 C5 C3 N2
<YLY 713>: H4 N1 C2 N2
<YLY 713>: C5 H1 N5 H2
<YLY 713>: H3 N3 C4 N4
<YLY 713>: C3 N1 C1 N3
<YLY 713>: C6 C1 N1 C2
<YLY 713>: C12 O8 C11 O3
<YLY 713>: C18 N7 C17 O9
<YLY 713>: C20 H31 C19 N8
total 2642 improper torsions applied
20 improper torsions in old prep form
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CASN 2
NLEU 2
WAT 38029
)
(no restraints)
Quit
i.e there is an unperturbed charge. However when I take the ligand+protein it
requires 12 Na ions and protein + trna requires 142 Na ions and the charges are
neutralized perfectly. However, when I take the full complex it adds only 153 Na
ions leaving a net charge of -0.999. Can this be a source of the problem as
described below?
Please help me out with this. Am I missing something obvious?
Sincere Regards,
Moitrayee
------------------------------- Original Message -------------------------------
Subject: problem with minimization
From: moitrayee.mbu.iisc.ernet.in
Date: Thu, October 22, 2009 4:31 pm
To: amber.ambermd.org
--------------------------------------------------------------------------------
Dear Amber Users,
I want to simulate a protein-ligand-trna complex in its dimeric state. When I
prepare this pdb and subject it to leap for generation of .prmtop and .prmcrd
files, no error is shown. However, the system shows segmentation fault in
minimization step.
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
***** Processor 31
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 128074 Allocated: 8538
rank 31 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
exit status of rank 31: killed by signal 9
rank 15 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
exit status of rank 15: killed by signal 9
rank 7 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
exit status of rank 7: killed by signal 9
rank 0 in job 5 compute-0-5.local_33031 caused collective abort of all ranks
exit status of rank 0: killed by signal 9
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
sander.MPI 0000000000512DEF Unknown Unknown Unknown
sander.MPI 00000000006F0E54 Unknown Unknown Unknown
sander.MPI 00000000004BE957 Unknown Unknown Unknown
sander.MPI 00000000004B5AAD Unknown Unknown Unknown
sander.MPI 0000000000407B22 Unknown Unknown Unknown
libc.so.6 000000332471C3FB Unknown Unknown Unknown
sander.MPI 0000000000407A6A Unknown Unknown Unknown
To check, I have seen that the protein+trna or the protein+ligand gives no such
error in the dimeric state. Again, there is no error in the full complex in the
monomeric state. Also, to check, I have taken protein and trna from both
subunits but ligand from just one subunit and no segmentation fault is seen
during minimization. I have repeated this for both the subunits.
Please help me out with your valuable suggestions. I am attaching my complete
pdb file. I am also attaching the parameter files for the ligand.
Thanks a lot in advance.
Sincere Regards,
Moitrayee
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Received on Thu Oct 22 2009 - 06:30:03 PDT
