Hi, Tom,
Thanks again for your reply. I have checked the H2 molecule, after 250
steps, the three atoms did end up not being linear which was not what I
wanted, so how can i solve this problem?
Thank you very much.
Rachel
On 11/2/06, darden <darden.gamera.niehs.nih.gov> wrote:
>
> rachel
> if ambpdb works for you---use it by all means--but i think the amber group
> intends to focus in the future on ptraj in place of these other analysis
> programs
>
> the ptraj way is fairly easy--you read in the prmtop and then say
> trajin restrt (where restrt is your ending coords from 250 steps)
> then trajout 250.pdb pdb (250.pdb will be your output file)
> see the ptraj documentation for further explanation
>
> even though your central DM atom has a vdw repulsion---if the hydrogen
> gets too close---its possible that the 1/r for coulomb wins over the
> 1/r^12 for vdw since the r in the vdw is the distance from DM which is
> greater by up to 0.7 angstroms----
>
> the problem is not there initially--since your energies are fine for the
> first 200 steps---somehow it ended up being pulled in and the DM repulsion
> is not big enough i'm guessing
>
> another possibility---but others may want to chime in---given you have no
> angular force term your H2 might end up not being linear in some
> electrostatic situations---also not sure if SHAKE is working on your
> DM-HH bonds--it may or may not be--in any case you may have a pretty
> wobbly H2 molecule which may not have the geometry you want---this can all
> be checked from pdb snap shots
>
> hope this helps
> tom darden
>
> On Thu, 2 Nov 2006, Rachel wrote:
>
> > Hi, Tom,
> >
> > Thanks very much for your reply. The HH atom has a positive charge of
> 0.475,
> > the hydrogen molecule model i wanted to use is Hunter's model, it is a
> three
> > point molecule with two atoms and a dummy placed in their midpoint, only
> the
> > two atoms have mass, and only the dummy has non-zero LJ parameters, both
> the
> > two atoms have +0.475 partial charge, and the dummy has -0.95 partial
> > charge, the bond distance is 0.7angstrom. I think the problem might
> caused
> > by some mistakes i built the hydrogen molecule, because i did the
> > minimization for the the same protein without the hydrogen molecule in
> it,
> > everything seems to be OK. Here is how i built the hydrogen molecule:
> >
> > I created it a pdb file with the coordinates (according to the bond
> > length) of the three atoms in it, and loaded the pdb into xleap, edited
> the
> > charges of the three atoms, saved as .lib, also i created the frcmod
> file
> > for this molecule, the following is how the frcmod file looks like:
> >
> >
> ----------------------------------------------------------------------------------------------------------------
> >
> > # H2 molecule parameters
> >
> > MASS
> > HH 1.008
> > DH 0.000
> >
> > BOND
> > HH-DH 0.0000 0.960
> >
> > ANGLE
> > HH-DH-HH 0.000 180.0
> >
> > DIHEDRAL
> >
> > IMPROPER
> >
> > NONBON
> > HH 0.000 0.000
> > DH 2.920 0.2722
> >
> >
> ----------------------------------------------------------------------------------------------------------------
> >
> > And also there are some Na+ in the system as well that used to
> neutralise
> > the protein, and the initial position of the HH atom was quite close to
> one
> > of the Na+, however, they are not positively charged?
> >
> > Also a question, as you suggested me to use ptraj to create the pdb file
> at
> > 300 steps, can i ask will there be any difference if i use ambpdb
> command
> > instead of ptraj?
> >
> > Thanks very much in advance for any suggestions ^_<
> >
> > Rachel
> >
> >
> > On 11/1/06, darden <darden.gamera.niehs.nih.gov> wrote:
> >>
> >> Dear Rachelle
> >>
> >> If it were me I would stop the minimization at 300 steps, convert back
> to
> >> a pdb file (ptraj) and look at the structure, particularly at close
> >> contacts involving your HH atom. Does your HH have a charge?
> >> How about its vdw parameters? Often hydrogens can get sucked into a
> >> "Coulomb singularity"; that is, the distance between it and some
> >> oppositely charged atom starts going to zero. Sometimes this is due to
> >> bad initial placement (too close to that oppositely charged atom atom
> to
> >> begin with) and sometimes to inadequate vdw repulsion for the hydrogen
> >> atom (nothing to stop Coulomb's law from pulling it in). Those are the
> 2
> >> causes I know of for your type of symptoms.
> >> hope this helps
> >> Tom Darden
> >>
> >> On Wed, 1 Nov 2006, Rachel wrote:
> >>
> >> > Dear AMBER users,
> >> >
> >> > I have a problem with my minimisation output, as u can see from the
> >> output
> >> > below, ,from 250 step, the EEL value started to oscillate bewteen
> about
> >> > (-2)*(10^6) to (-8)*(10^7) and then too big to fit the space, and the
> >> job
> >> > stopped with the error message as 'MPI process rank, caught a
> SIGSEGV'.
> >> As
> >> > can be seen, the problematic atom is atom 12159 which named HH (i
> made
> >> it
> >> > up), it is a hydrogen atom in a hydrogen molecule that i added in my
> >> system.
> >> >
> >> > Can anyone suggest me what shall I do to solve the problem?
> >> >
> >> > Thanks very much in advance!
> >> >
> >> > Rachel
> >> >
> >> > The following is the output:
> >> >
> >>
> >>
> -----------------------------------------------------------------------------------------------------------------------
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1 -1.8130E+05 8.6589E+00 1.2311E+03
> DH 12158
> >> >
> >> > BOND = 12319.3157 ANGLE = 4262.2942 DIHED =
> >> > 6788.2453
> >> > VDWAALS = 20966.0238 EEL = -264399.8765 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3817.5022 1-4 EEL = 34943.0628 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 50 -1.8625E+05 2.8188E+00 4.3913E+02
> FE 12110
> >> >
> >> > BOND = 11794.4274 ANGLE = 3181.7918 DIHED =
> >> > 6832.5737
> >> > VDWAALS = 18284.3228 EEL = -264556.0346 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3581.8939 1-4 EEL = 34629.6021 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 100 -1.8731E+05 1.4581E+00 8.3876E+01
> FE 12110
> >> >
> >> > BOND = 11728.4379 ANGLE = 2852.5435 DIHED =
> >> > 6858.0073
> >> > VDWAALS = 17976.7772 EEL = -264680.1459 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3457.5692 1-4 EEL = 34495.5597 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 150 -1.8797E+05 1.2138E+00 9.3236E+01
> FE 12110
> >> >
> >> > BOND = 11714.1093 ANGLE = 2680.6319 DIHED =
> >> > 6875.7728
> >> > VDWAALS = 17802.4798 EEL = -264805.0722 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3365.2133 1-4 EEL = 34401.7260 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 200 -1.8844E+05 1.4438E+00 2.2334E+02
> FE 12110
> >> >
> >> > BOND = 11713.6752 ANGLE = 2577.4489 DIHED =
> >> > 6887.9989
> >> > VDWAALS = 17693.9506 EEL = -264938.4370 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3294.3797 1-4 EEL = 34332.7427 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 250 -1.4001E+07 2.2874E+10 5.3567E+12 CB
> 1710
> >> >
> >> > BOND = 11724.6116 ANGLE = 2552.7526 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7588 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 300 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4454 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 350 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.4475 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 400 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 450 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4465 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 500 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.4796 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 550 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 600 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4483 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 650 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.5746 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 700 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 750 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4500 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 800 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.5853 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 850 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 900 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4488 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 950 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.6284 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1000 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1050 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4489 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1100 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.6596 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1150 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1200 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4602 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1250 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.8262 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1300 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1350 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4600 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1400 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.7398 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1450 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1500 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4562 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1550 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.7172 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1600 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1650 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4629 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1700 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.8409 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1750 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1800 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4659 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1850 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.9068 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1900 -2.1791E+07 5.5955E+10 1.3104E+13
> HH 12159
> >> >
> >> > BOND = 11724.6114 ANGLE = 2552.7524 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = ************* HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 1950 -1.9550E+06 3.7414E+08 8.7616E+10
> HH 12159
> >> >
> >> > BOND = 11724.6105 ANGLE = 2552.7517 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7584 EEL = -2031379.4671 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >> > NSTEP ENERGY RMS GMAX
> NAME NUMBER
> >> > 2000 -8.4332E+06 8.1505E+09 1.9087E+12
> HH 12159
> >> >
> >> > BOND = 11724.6113 ANGLE = 2552.7523 DIHED =
> >> > 6892.6022
> >> > VDWAALS = 17660.7587 EEL = -8509648.9202 HBOND =
> >> > 0.0000
> >> > 1-4 VDW = 3265.4012 1-4 EEL = 34305.5080 RESTRAINT =
> >> > 0.0000
> >> >
> >> >
> >>
> >>
> --------------------------------------------------------------------------------------------------------------------------------------
> >> >
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber.scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >>
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 05 2006 - 06:07:41 PST
