AMBER Archive (2006)

Subject: Re: AMBER: too big EEL values in the minimisation output

From: Rachel (comeonsos_at_googlemail.com)
Date: Thu Nov 02 2006 - 12:08:00 CST

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_at_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
> >
> >
> --------------------------------------------------------------------------------------------------------------------------------------
> >
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