The type of H54 is HO 'hydroxyl group' within parm99. And in my molecule it is
attached to the oxygen which is part of the sulfate group, -SO3H. I have
introduced the atom type for the S atom. And O41 is OS in parm99 too. The
positions of H54 and O41 are like this R-O41-SO3H54. Both of the parms of H54
and O41 are from Parm99. Do I need to modify the VDW parm? Thanks
Lan
Quoting Michael George Lerner <mlerner.umich.edu>:
>
> 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
>
> --
> This isn't a democracy;| _ |Michael Lerner
> it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan
> -Torrence, Bring It On| - against HTML email X | Biophysics
> | / \ | mlerner.umich
>
> 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 - 17:53:00 PST
