AMBER Archive (2007)

Subject: Re: AMBER: Sander Error

From: Colby C (colbychiauzzi_at_gmail.com)
Date: Tue Jul 03 2007 - 13:21:18 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 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
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>
>
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