Re: AMBER: Close contact warnings

From: Michael George Lerner <mlerner.umich.edu>
Date: Wed, 18 Feb 2004 08:58:50 -0500 (EST)

Hi,

I missed the first bit of this discussion, so I don't know what molecule
you're working with, but .. what is the atom type of H54? Does it have
any van der Waals parameters? It's possible that it has a charge, but no
van der Waals parameter, which would cause the H and O to want to sit on
top of eachother. Note that your VDWAALS energy hasn't changed much
between 388 and 389, but it certainly *should* if the H and O are directly
on top of eachother.

When I ran into this problem, I was actually able just ignore the
Hydrogen. If you can't do that, you probably want to give it a small van
der Waals parameter.

Then again, like I said, I missed the first bit of this discussion, so I
might be completely wrong :).

-michael

--
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On Wed, 18 Feb 2004, L Jin wrote:
> I checked the output file carefully and found that from step 388 to 389
> something strange happened:
>
>
>   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>     388      -1.5636E+02     4.2407E+00     1.7222E+01     H54        51
>
>  BOND    =       11.7069  ANGLE   =       77.0644  DIHED      =       51.9480
>  VDWAALS =      -11.8319  EEL     =     -312.5510  HBOND      =        0.0000
>  1-4 VDW =       12.5818  1-4 EEL =       14.7250  RESTRAINT  =        0.0000
>
>
>    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
>     389      -1.0020E+01     7.7049E+01     4.4229E+02     H54        51
>
>  BOND    =      161.0069  ANGLE   =      168.0122  DIHED      =       51.8140
>  VDWAALS =      -12.2718  EEL     =     -303.3282  HBOND      =        0.0000
>  1-4 VDW =       12.8826  1-4 EEL =      -88.1358  RESTRAINT  =        0.0000
>
>
> I ran another 440 steps minimization just before the clash one (step 448). I got
> the pdb file from the restrt and prmtop and loaded it to xleap. I found that H54
> and O41 become one point, which should be two seperated atoms. This tendency
> happened from step 389. I do not know why it happened. Is there any method to
> avoid this? Thanks a lot.
>
> Lan
>
>
>
>
>
>
>
>
>
> Quoting "David A. Case" <case.scripps.edu>:
>
> > On Tue, Feb 17, 2004, L Jin wrote:
> > >
> > >  minimization with sander (Amber7)
> > >  &cntrl
> > >   imin = 1, maxcyc = 500, drms = 0.0005, ntb = 0,
> > >   ntpr = 1, cut = 999., ncyc = 100,
> > >  &end
> >
> > Have you looked visually at your molecule? Clearly, something very unusual
> > is going on.  You converge smoothly to a total energy of around -146 at
> > step 329, with an rms gradient that is not too large:
> > >
> > >
> > >    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
> > >     329      -1.4583E+02     1.1848E+00     4.6123E+00     C31        42
> > >
> > >  BOND    =        4.5116  ANGLE   =       48.5651  DIHED      =
> > 44.7987
> > >  VDWAALS =      -11.6564  EEL     =     -312.0418  HBOND      =
> > 0.0000
> > >  1-4 VDW =       12.4566  1-4 EEL =       67.5408  RESTRAINT  =
> > 0.0000
> > >
> > Then something bad happens by step 445; the energy has risen to 0.6, and
> > the rms gradient is up to 49.  Note that the bond energy especially is
> > now very high:
> >
> > >   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
> > >     445       5.9643E-01     4.9484E+01     3.4419E+02     O41        48
> > >
> > >  BOND    =      118.4773  ANGLE   =      120.6025  DIHED      =
> > 53.2918
> > >  VDWAALS =      -12.3050  EEL     =     -305.5181  HBOND      =
> > 0.0000
> > >  1-4 VDW =       12.2175  1-4 EEL =       13.8304  RESTRAINT  =
> > 0.0000
> > >
> >
> > After this, things get very bad quickly, with some 1-4 contact getting
> > very short:
> >
> > >
> > >    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
> > >     446      -2.5247E+03     7.9332E+03     5.2102E+04     O41        48
> > >
> > >  BOND    =      119.2712  ANGLE   =      146.2262  DIHED      =
> > 52.5048
> > >  VDWAALS =      -12.2562  EEL     =     -302.8007  HBOND      =
> > 0.0000
> > >  1-4 VDW =       12.4022  1-4 EEL =    -2540.0104  RESTRAINT  =
> > 0.0000
> > >
> > >
> > >    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
> > >     447      -3.0601E+05     1.0647E+08     8.2860E+08     H54        51
> > >
> > >  BOND    =      120.7894  ANGLE   =      148.1497  DIHED      =
> > 52.4627
> > >  VDWAALS =      -12.2550  EEL     =     -302.7370  HBOND      =
> > 0.0000
> > >  1-4 VDW =       12.4228  1-4 EEL =  -306025.0251  RESTRAINT  =
> > 0.0000
> > >
> > >
> > >    NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
> > >     448      -3.1064E+05     1.0972E+08     8.2030E+08     H54        51
> > >
> > >  BOND    =      120.7918  ANGLE   =      148.1526  DIHED      =
> > 52.4626
> > >  VDWAALS =      -12.2549  EEL     =     -302.7369  HBOND      =
> > 0.0000
> > >  1-4 VDW =       12.4228  1-4 EEL =  -310660.0186  RESTRAINT  =
> > 0.0000
> >
> >
> > You need to examine your structure carefully (especially around
> > atom H54, or maybe around atom O41).  I suspect you have something
> > "non-chemical" going on.
> >
> > ...regards...dac
> >
> > --
> >
> > ==================================================================
> > David A. Case                     |  e-mail:      case.scripps.edu
> > Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
> > The Scripps Research Institute    |  phone:        +1-858-784-9768
> > 10550 N. Torrey Pines Rd.         |  home page:
> > La Jolla CA 92037  USA            |    http://www.scripps.edu/case
> > ==================================================================
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Received on Wed Feb 18 2004 - 14:53:00 PST