AMBER Archive (2007)

Subject: Re: AMBER: Sander Error

From: Colby C (colbychiauzzi_at_gmail.com)
Date: Mon Jul 09 2007 - 10:39:50 CDT

We have figured out that our problem is with the ligands. We are
trying to do the plain minimization of just the 1 ligand in vacuum or
in water. When can successfully make the 2 input files for SANDER
with no apparent error. When we minimized in vacuum we used this .in
file

 &cntrl
 imin = 1,
 maxcyc = 150,
 ntb = 0,
 igb = 0,
 cut = 12
 /

Here is our error

  NSTEP ENERGY RMS GMAX NAME NUMBER
   100 -7.3954E+03 4.9857E+04 3.4004E+05 O1P 52

 BOND = 81.2786 ANGLE = 147.6936 DIHED = 39.9517
 VDWAALS = -6.0557 EEL = 162.0704 HBOND = 0.0000
 1-4 VDW = 16.4457 1-4 EEL = -7836.8036 RESTRAINT = 0.0000
 Frac coord min, max: -0.01100395540206483 0.8458959681694271
 The system has extended beyond
    the extent of the virtual box.
 Restarting sander will recalculate
   a new virtual box with 30 Angstroms
   extra on each side, if there is a
   restart file for this configuration.
 SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
 Atom out of bounds. If a restart has been written,
 restarting should resolve the error

If we change the maxcyc to 95, the minimization completes. When we
output the resulting .pdb file we can see that the 2 Oxygens from the
PO(OH)2 groups have collided into each other.

If we put our ligand in a TIP3PBOX and run this .in file

Test run 1
 &cntrl
    IMIN = 1, NCYC = 250, MAXCYC = 300
 /

Minimization completes. In the resulting .pdb files we can see that
the Oxygens are starting to collide again. If we change maxcyc to 500
we get this error in our cygwin screen

$ ./sander -O -i MO3.in -o MO3.out -c MO3.inpcrd -p MO3.prmtop -r MO3.rst
     6 [main] sander 3536 _cygtls::handle_exceptions: Error while
dumping state (probably corrupted
 stack)
Segmentation fault (core dumped)

This is our prepin file of the Ligand

   0 0 2

This is a remark line
molecule.res
MO3 INT 0
CORRECT OMIT DU BEG
 0.0000
  1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
  2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
  3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
  4 O12 oh M 3 2 1 1.540 111.208 180.000 -0.60103
  5 H12 ho E 4 3 2 0.968 66.946 17.987 0.40790
  6 C12 c3 M 4 3 2 1.421 119.606 -77.899 0.10250
  7 H10 h1 E 6 4 3 1.090 108.639 101.954 0.04969
  8 H11 h1 E 6 4 3 1.090 108.611 -140.083 0.08024
  9 C11 c3 M 6 4 3 1.534 110.311 -19.082 0.10941
 10 O11 oh S 9 6 4 1.425 108.031 85.662 -0.61496
 11 H13 ho E 10 9 6 0.968 108.059 -86.657 0.42780
 12 H9 h1 E 9 6 4 1.090 107.523 -31.466 0.05020
 13 C10 c3 M 9 6 4 1.546 114.710 -151.857 0.11886
 14 O10 oh S 13 9 6 1.427 109.546 -42.974 -0.59954
 15 H8 ho E 14 13 9 0.969 107.384 -125.769 0.42123
 16 H7 h1 E 13 9 6 1.090 104.298 -160.020 0.05260
 17 C9 c3 M 13 9 6 1.548 114.382 80.384 0.08589
 18 O9 oh S 17 13 9 1.424 109.413 163.328 -0.62464
 19 H14 ho E 18 17 13 0.964 102.621 -50.290 0.42057
 20 H6 h1 E 17 13 9 1.090 104.945 50.688 0.08532
 21 C8 c3 M 17 13 9 1.543 113.673 -74.131 0.20963
 22 H4 h1 E 21 17 13 1.090 107.727 -62.284 0.06823
 23 H5 h1 E 21 17 13 1.090 107.718 57.045 0.07025
 24 N7 nh M 21 17 13 1.485 114.157 177.376 -0.78077
 25 H3 hn E 24 21 17 1.026 117.060 -93.629 0.45011
 26 C6 cc M 24 21 17 1.420 122.697 111.522 0.34527
 27 N1 n M 26 24 21 1.458 117.509 -63.637 -0.48531
 28 H1 hn E 27 26 24 1.020 121.781 4.727 0.37198
 29 C2 c M 27 26 24 1.349 121.734 -178.982 0.81393
 30 O2 o E 29 27 26 1.224 118.848 178.174 -0.64551
 31 N3 n M 29 27 26 1.348 120.684 -1.023 -0.58613
 32 H2 hn E 31 29 27 1.030 118.084 -178.718 0.35330
 33 C4 c M 31 29 27 1.356 123.843 1.274 0.73613
 34 O4 o E 33 31 29 1.230 118.954 176.995 -0.63018
 35 C5 cd M 33 31 29 1.570 117.568 -1.231 -0.36352
 36 C13 c3 M 35 33 31 1.530 117.391 -178.791 -0.00568
 37 H15 hc E 36 35 33 1.090 112.423 149.517 0.02855
 38 H16 hc E 36 35 33 1.090 112.396 29.516 0.07876
 39 C14 c3 M 36 35 33 1.540 112.411 -90.471 -0.08300
 40 H17 hc E 39 36 35 1.090 111.480 83.248 0.05702
 41 H18 hc E 39 36 35 1.090 111.467 -36.724 0.03359
 42 C15 c3 M 39 36 35 1.537 111.461 -156.739 -0.08690
 43 H19 hc E 42 39 36 1.090 111.892 116.907 0.04175
 44 H20 hc E 42 39 36 1.090 111.908 -3.062 0.04198
 45 C16 c3 M 42 39 36 1.538 111.918 -123.077 -0.07876
 46 H21 hc E 45 42 39 1.090 111.351 46.283 0.04818
 47 H22 hc E 45 42 39 1.090 111.344 -73.689 0.04706
 48 C17 c3 M 45 42 39 1.537 111.359 166.297 -0.07064
 49 H23 hc E 48 45 42 1.090 112.365 134.368 0.05216
 50 H24 hc E 48 45 42 1.089 112.342 14.334 0.07193
 51 C1 c3 M 48 45 42 1.540 112.361 -105.652 -0.40487
 52 H25 hc E 51 48 45 1.090 107.763 33.212 0.12843
 53 H26 hc E 51 48 45 1.090 107.759 -86.778 0.12295
 54 P p5 M 51 48 45 1.733 116.411 153.248 1.56656
 55 O1P o E 54 51 48 1.537 113.885 -34.591 -0.86754
 56 O2P oh S 54 51 48 1.538 111.185 86.721 -0.78742
 57 H28 ho E 56 54 51 0.970 104.646 -80.235 0.47704
 58 O3P oh M 54 51 48 1.592 106.584 -155.438 -0.78774
 59 H27 ho E 58 54 51 1.049 109.498 178.695 0.47716

LOOP
  C5 C6

IMPROPER
  C8 C6 N7 H3
  C5 N1 C6 N7
  C2 C6 N1 H1
  N1 N3 C2 O2
  C2 C4 N3 H2
  C5 N3 C4 O4
  C4 C13 C5 C6

DONE
STOP

On 7/3/07, Colby C <colbychiauzzi_at_gmail.com> wrote:
> We have figured out that our problem is with the ligands. We are
> trying to do the plain minimization of just the 1 ligand in vacuum or
> in water. When can successfully make the 2 input files for SANDER
> with no apparent error. When we minimized in vacuum we used this .in
> file
>
>
> &cntrl
> imin = 1,
> maxcyc = 150,
> ntb = 0,
> igb = 0,
> cut = 12
> /
>
>
> Here is our error
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 100 -7.3954E+03 4.9857E+04 3.4004E+05 O1P 52
>
> BOND = 81.2786 ANGLE = 147.6936 DIHED = 39.9517
> VDWAALS = -6.0557 EEL = 162.0704 HBOND = 0.0000
> 1-4 VDW = 16.4457 1-4 EEL = -7836.8036 RESTRAINT = 0.0000
> Frac coord min, max: -0.01100395540206483 0.8458959681694271
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
>
> If we change the maxcyc to 95, the minimization completes. When we
> output the resulting .pdb file we can see that the 2 Oxygens from the
> PO(OH)2 groups have collided into each other.
>
>
>
> If we put our ligand in a TIP3PBOX and run this .in file
>
> Test run 1
> &cntrl
> IMIN = 1, NCYC = 250, MAXCYC = 300
> /
>
> Minimization completes. In the resulting .pdb files we can see that
> the Oxygens are starting to collide again. If we change maxcyc to 500
> we get this error in our cygwin screen
>
> $ ./sander -O -i MO3.in -o MO3.out -c MO3.inpcrd -p MO3.prmtop -r MO3.rst
> 6 [main] sander 3536 _cygtls::handle_exceptions: Error while
> dumping state (probably corrupted
> stack)
> Segmentation fault (core dumped)
>
>
>
>
> This is our prepin file of the Ligand
>
>
> 0 0 2
>
> This is a remark line
> molecule.res
> MO3 INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 O12 oh M 3 2 1 1.540 111.208 180.000 -0.60103
> 5 H12 ho E 4 3 2 0.968 66.946 17.987 0.40790
> 6 C12 c3 M 4 3 2 1.421 119.606 -77.899 0.10250
> 7 H10 h1 E 6 4 3 1.090 108.639 101.954 0.04969
> 8 H11 h1 E 6 4 3 1.090 108.611 -140.083 0.08024
> 9 C11 c3 M 6 4 3 1.534 110.311 -19.082 0.10941
> 10 O11 oh S 9 6 4 1.425 108.031 85.662 -0.61496
> 11 H13 ho E 10 9 6 0.968 108.059 -86.657 0.42780
> 12 H9 h1 E 9 6 4 1.090 107.523 -31.466 0.05020
> 13 C10 c3 M 9 6 4 1.546 114.710 -151.857 0.11886
> 14 O10 oh S 13 9 6 1.427 109.546 -42.974 -0.59954
> 15 H8 ho E 14 13 9 0.969 107.384 -125.769 0.42123
> 16 H7 h1 E 13 9 6 1.090 104.298 -160.020 0.05260
> 17 C9 c3 M 13 9 6 1.548 114.382 80.384 0.08589
> 18 O9 oh S 17 13 9 1.424 109.413 163.328 -0.62464
> 19 H14 ho E 18 17 13 0.964 102.621 -50.290 0.42057
> 20 H6 h1 E 17 13 9 1.090 104.945 50.688 0.08532
> 21 C8 c3 M 17 13 9 1.543 113.673 -74.131 0.20963
> 22 H4 h1 E 21 17 13 1.090 107.727 -62.284 0.06823
> 23 H5 h1 E 21 17 13 1.090 107.718 57.045 0.07025
> 24 N7 nh M 21 17 13 1.485 114.157 177.376 -0.78077
> 25 H3 hn E 24 21 17 1.026 117.060 -93.629 0.45011
> 26 C6 cc M 24 21 17 1.420 122.697 111.522 0.34527
> 27 N1 n M 26 24 21 1.458 117.509 -63.637 -0.48531
> 28 H1 hn E 27 26 24 1.020 121.781 4.727 0.37198
> 29 C2 c M 27 26 24 1.349 121.734 -178.982 0.81393
> 30 O2 o E 29 27 26 1.224 118.848 178.174 -0.64551
> 31 N3 n M 29 27 26 1.348 120.684 -1.023 -0.58613
> 32 H2 hn E 31 29 27 1.030 118.084 -178.718 0.35330
> 33 C4 c M 31 29 27 1.356 123.843 1.274 0.73613
> 34 O4 o E 33 31 29 1.230 118.954 176.995 -0.63018
> 35 C5 cd M 33 31 29 1.570 117.568 -1.231 -0.36352
> 36 C13 c3 M 35 33 31 1.530 117.391 -178.791 -0.00568
> 37 H15 hc E 36 35 33 1.090 112.423 149.517 0.02855
> 38 H16 hc E 36 35 33 1.090 112.396 29.516 0.07876
> 39 C14 c3 M 36 35 33 1.540 112.411 -90.471 -0.08300
> 40 H17 hc E 39 36 35 1.090 111.480 83.248 0.05702
> 41 H18 hc E 39 36 35 1.090 111.467 -36.724 0.03359
> 42 C15 c3 M 39 36 35 1.537 111.461 -156.739 -0.08690
> 43 H19 hc E 42 39 36 1.090 111.892 116.907 0.04175
> 44 H20 hc E 42 39 36 1.090 111.908 -3.062 0.04198
> 45 C16 c3 M 42 39 36 1.538 111.918 -123.077 -0.07876
> 46 H21 hc E 45 42 39 1.090 111.351 46.283 0.04818
> 47 H22 hc E 45 42 39 1.090 111.344 -73.689 0.04706
> 48 C17 c3 M 45 42 39 1.537 111.359 166.297 -0.07064
> 49 H23 hc E 48 45 42 1.090 112.365 134.368 0.05216
> 50 H24 hc E 48 45 42 1.089 112.342 14.334 0.07193
> 51 C1 c3 M 48 45 42 1.540 112.361 -105.652 -0.40487
> 52 H25 hc E 51 48 45 1.090 107.763 33.212 0.12843
> 53 H26 hc E 51 48 45 1.090 107.759 -86.778 0.12295
> 54 P p5 M 51 48 45 1.733 116.411 153.248 1.56656
> 55 O1P o E 54 51 48 1.537 113.885 -34.591 -0.86754
> 56 O2P oh S 54 51 48 1.538 111.185 86.721 -0.78742
> 57 H28 ho E 56 54 51 0.970 104.646 -80.235 0.47704
> 58 O3P oh M 54 51 48 1.592 106.584 -155.438 -0.78774
> 59 H27 ho E 58 54 51 1.049 109.498 178.695 0.47716
>
>
> LOOP
> C5 C6
>
> IMPROPER
> C8 C6 N7 H3
> C5 N1 C6 N7
> C2 C6 N1 H1
> N1 N3 C2 O2
> C2 C4 N3 H2
> C5 N3 C4 O4
> C4 C13 C5 C6
>
> DONE
> STOP
>
>
>
>
>
>
>
>
>
>
>
>
> On 6/29/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> >
> > > We are trying to minimize 5 ligands in protein . The minimization in
> > > SANDER works for just the protein but when we run SANDER with the
> > > ligands we get this error
> >
> > > The system has extended beyond
> > > the extent of the virtual box.
> >
> > > &cntrl
> > > imin = 1,
> > > maxcyc = 500,
> > > ncyc = 250,
> > > ntb = 0,
> > > igb = 0,
> > > cut = 12
> > > /
> >
> > If this is happening during minimization then it should tell you that
> > something is very very wrong with your starting structure. Do you really
> > expect an atom to move by 30 angstroms during minimization? Take a careful
> > look at the actual output, I bet you have some huge energy and consequently
> > a huge force. Look at the RMS and GMAX entries and in particular the atom
> > number of the atom with the maximum force that is printed. Then visualy
> > inspect your starting structure and then perhaps you will see the problem.
> >
> > In addition are you certain you want a gas phase minimum? If so then fine
> > but you have to realize that there is no reason why your protein and ligand
> > should actually be stable in a vacuum... This is an aside however, firstly
> > you need to fix the structural defects in your starting structure. If you
> > can't find anything wrong here then carefully check the parameters you are
> > using - do you have some equilibrium bond length set to some crazy long
> > value?
> >
> > Good luck...
> >
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> > be read every day, and should not be used for urgent or sensitive issues.
> >
> >
> > -----------------------------------------------------------------------
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> >
>
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