Hi Bill,
My apologies that I didn't respond to your email. I looked at the atoms
which showed high gradient in energy minimization.
I do not see any overlap/problem with any neighbouring atoms in the
starting structure. However, when I visualise min.rst after first step I
could see that bond lengths, radius isn't right compared to the original
structure. All atoms/bonds look dismantled.
On 18 August 2016 at 18:36, Bill Ross <ross.cgl.ucsf.edu> wrote:
> You don't mention whether you tried the last suggestion below, or the
> one I gave twice and could be applied to your output below.
>
> Bill
>
>
> On 8/18/16 1:27 AM, Neha Gandhi wrote:
> > I tried several things and still I am not able to figure out issue with
> > minimisation of supercell of HAP. I am using AMBER16.
> >
> > Here is the detailed procedure I am following. My apologies for a long
> > email.
> >
> > I would appreciate some help.
> > Many thanks,
> > Neha
> >
> >
> >
> >
> > I have a pdb file of a unit cell and I am converting using antechamber to
> > mol2 file
> >
> > antechamber -fi pdb -i input.pdb -fo mol2 -o input.mol2 -rn
> >
> > I manually edit the atomtypes and charges in the input.mol2 file based on
> > the interface force field. I define these new atom types in leaprc.hap.
> >
> > logFile leap.log
> > addAtomTypes {
> > { "oap1" "O" "sp3" }
> > { "oap2" "O" "sp3" }
> > { "hop" "H" "sp3" }
> > { "pap" "P" "sp3" }
> > { "NG" "Ca" "sp3" }
> > }
> >
> >
> > I prepare frcmod file as below where NG is calcium ion.
> >
> >
> > Bonded parameters and revised vdW parameters for hydroxyapatite
> (frcmod.hap)
> >
> > MASS
> > NG 40.08
> > pap 30.97380
> > oap0 16.00
> > oap1 16.00
> > oap2 16.00
> > hop 1.007970
> >
> >
> > BOND
> > pap-oap0 430.0 1.570 from HO-OH
> > pap-oap1 430.0 1.570 from HO-OH
> > oap2-hop 500.0 0.940 from O2-P
> >
> > ANGLE
> > oap0-pap-oap1 109.47 125
> > oap1-pap-oap1 109.47 125
> > pap-oap1-hop -115.0 50
> >
> > DIHE
> >
> > IMPR
> >
> > NONB
> > NG 3.30 0.130
> > pap 4.30 0.280
> > oap0 3.40 0.070
> > oap1 3.40 0.070
> > oap2 3.70 0.080
> > hop 0.0001 0
> >
> >>> $AMBERHOME/bin/tleap -s -f leaprc.ff99SBildn
> >>> source leaprc.hap
> >> HAP=loadmol2 input.mol2
> >> loadamberparams frcmod.hap
> >> saveoff HAP hap.lib
> >> check HAP
> >> quit
> > I prepare supercell from the input file which has unit cell information
> > PropPDB -p input.pdb -o supercell.pdb -ix 15 -iy 9 -iz 4
> >
> >>> $AMBERHOME/bin/tleap -s -f leaprc.ff99SBildn
> >> source leaprc.hap
> >> loadamberparams frcmod.hap
> >> loadoff hap.lib
> >> m1=loadpdb supercell.pdb
> >> set m1 box {145 150 39}
> >> set default nocenter on
> >> saveamberparm m1 supercell.inpcrd supercell.prmtop
> > ChBox -c supercell.inpcrd -o correct.inpcrd -X 145 -Y 150 -Z 39 -al 90.0
> > -bt 90.0 -gm 90.0
> >
> > When I visualise the topology in chimera, it looks fine. I also run check
> > in cpptraj
> >
> > cpptraj -p supercell.prmtop -i ptraj.in
> > ---
> > trajin correct.inpcrd
> > check reportfile report.dat
> >
> > The report.dat file is empty so I assume there are no overlaps.
> >
> > I try to run minimization using pmemd.MPI and that's where I am not able
> to
> > figure out why the structure shows high energies and min.rst file doesn't
> > look right. I convert min.rst file using cpptraj to pdb. It seems that
> > calcium ion (NG) is interpreted as carbon or some other atoms and hence I
> > see all steric clashes with the oxygens. The initial topology and
> > coordinate didn't show any overlaps (I also visualised in Discovery
> Studio
> > and Chimera).
> >
> > Here is my minimization script
> > &cntrl
> >
> > imin =
> > 1,ntmin=2,
> > maxcyc =
> > 1000,
> > ncyc =
> > 500,
> > cut =
> > 11,ntb=1,
> > ntr=1,
> > restraintmask=":HAP",
> >
> > restraint_wt=100,
> > /
> >
> > This is the output of minimization:
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 5.0304E+14 8.1452E+11 1.2428E+13 O73 34894
> >
> > BOND = 46748.9087 ANGLE = 318386.7121 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4000046.6466 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 0.0000
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 50 2.2497E+11 9.5325E+07 3.3182E+09 CA30 28506
> >
> > BOND = 772861.1189 ANGLE = 489832.3379 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4567131.5327 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 933846.7563
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 100 9.2042E+09 5.3304E+05 2.7526E+07 O31 6171
> >
> > BOND = 2420450.1677 ANGLE = 756533.3318 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4635513.6335 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 4359080.5311
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 150 3.0328E+09 9.4245E+04 7.1836E+05 O31 187
> >
> > BOND = 3808312.7141 ANGLE = 863774.1317 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4543979.1475 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 9532589.6273
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 200 1.4703E+09 3.6367E+04 1.6077E+06 CA17 6197
> >
> > BOND = 5867323.1094 ANGLE = 1174149.1844 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4417485.8014 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 16435227.5152
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 250 9.4494E+08 1.8290E+04 1.2297E+06 CA22 6498
> >
> > BOND = 8314379.0384 ANGLE = 1463930.5938 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4306716.0676 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 23916270.3583
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 300 6.7807E+08 9.1264E+03 9.8786E+04 O103 41333
> >
> > BOND = 11086364.2336 ANGLE = 1747733.5268 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4212789.8325 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 33123794.4242
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 350 5.5606E+08 1.6580E+04 3.6162E+06 O13 12412
> >
> > BOND = 13220177.3840 ANGLE = 2031579.5402 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4165416.4102 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 41585009.6542
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 400 4.7793E+08 8.5694E+04 1.2868E+07 CA17 12445
> >
> > BOND = 15083792.1595 ANGLE = 2362636.3194 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4123963.9025 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 50917778.4003
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 450 4.1072E+08 6.2840E+04 1.3156E+07 O3 16101
> >
> > BOND = 16927718.9339 ANGLE = 2696951.0744 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4078061.5810 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 63016293.0525
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 500 3.8481E+08 2.0123E+05 4.2818E+07 CA12 44472
> >
> > BOND = 17844656.1654 ANGLE = 2894325.7448 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4043711.6748 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 71910687.9749
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 550 3.5528E+08 2.0033E+04 4.1273E+06 CA11 207
> >
> > BOND = 18472587.3852 ANGLE = 2983080.9756 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -4003270.5618 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 82047155.8306
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 600 3.3771E+08 1.3592E+03 9.9758E+04 CA13 31449
> >
> > BOND = 18681793.1570 ANGLE = 2895988.1770 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3956649.3711 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > 91980473.4298
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 650 3.2769E+08 7.2663E+02 4.7907E+04 O13 6164
> >
> > BOND = 18529998.1978 ANGLE = 2752344.0658 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3910263.6521 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 700 3.2206E+08 9.1785E+02 1.0210E+05 O114 21979
> >
> > BOND = 18153361.9508 ANGLE = 2652842.4367 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3870863.5750 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 750 3.1948E+08 1.2452E+04 2.5123E+06 O4 28687
> >
> > BOND = 17777425.0388 ANGLE = 2565639.6862 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3843271.2281 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 800 3.1658E+08 2.8941E+02 1.6874E+04 O4 31855
> >
> > BOND = 17470242.2855 ANGLE = 2511026.7739 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3821236.6015 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 850 3.1486E+08 6.0124E+02 9.3354E+04 O4 25519
> >
> > BOND = 17215714.5258 ANGLE = 2476035.7035 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3804324.2469 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 900 3.1366E+08 7.8516E+02 9.7218E+04 CA16 9364
> >
> > BOND = 17029172.3465 ANGLE = 2453714.2151 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3785496.4677 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 950 3.1266E+08 3.2197E+02 2.4683E+04 CA13 38137
> >
> > BOND = 16892215.1494 ANGLE = 2430390.5972 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3773586.1387 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> > EAMBER = *************
> >
> >
> > NSTEP ENERGY RMS GMAX NAME
> NUMBER
> > 1000 3.1185E+08 5.7211E+02 9.4441E+04 CA21 38265
> >
> > BOND = 16790846.7890 ANGLE = 2413392.6551 DIHED =
> > 0.0000
> > VDWAALS = ************* EEL = -3762616.6050 HBOND =
> > 0.0000
> > 1-4 VDW = 0.0000 1-4 EEL = 0.0000 RESTRAINT =
> > *************
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On 17 August 2016 at 00:58, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> >> On Tue, Aug 16, 2016 at 7:17 AM, Neha Gandhi <n.gandhiau.gmail.com>
> wrote:
> >>> To check for the structure or overlaps I issued following command in
> >>> cpptraj script
> >>>
> >>> trajin supercell.pdb
> >>> checkoverlap reportfile report.dat
> >>>
> >> You'll want to run the 'check' command on the actual topology and
> >> restart that gives you the strange energies, not the PDB.
> >>
> >> -Dan
> >>
> >>> Alternatively I also performed check command after loading
> supercell.pdb
> >> in
> >>> the tleap file.
> >>>
> >>> No information on steric clashes/overlaps were reported. I also
> >> visulaised
> >>> the structure in Discovery studio and no clashes/overlaps were found.
> >>>
> >>> I tested a smaller cell 2x2x2 using same method above and I manually
> >>> increase the box size in the inpcrd file as compared to the one
> assigned
> >> by
> >>> tleap. This successfully finished minimization. I will try changing box
> >>> size of supercell tomorrow and see if it can successfully run.
> >>>
> >>> Cheers,
> >>> Neha
> >>>
> >>>
> >>>
> >>>
> >>> On 16 August 2016 at 22:04, David A Case <david.case.rutgers.edu>
> wrote:
> >>>
> >>>> On Tue, Aug 16, 2016, Neha Gandhi wrote:
> >>>>
> >>>>> I did minimization on a unit cell of HAP. It works fine with or
> >> without
> >>>>> restraints. The trouble starts when I prepare a supercell 15x15x4
> >> size.
> >>>> What, exactly, did you do to "prepare a supercell 15x15x4 size"?
> >>>>
> >>>> Also, how, exactly, did you you conclude that there were no overlaps
> in
> >>>> your
> >>>> structure?
> >>>>
> >>>> Remember to try to report exactly what you did (what the commands
> were,
> >>>> what
> >>>> the results were). What you have been reporting is what you intended
> >>>> to do, which might not (in this case: probably does not) correspond
> with
> >>>> what
> >>>> you actually did.
> >>>>
> >>>> ...dac
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>> --
> >>> Regards,
> >>> Dr. Neha S. Gandhi,
> >>> Vice Chancellor's Research Fellow,
> >>> Queensland University of Technology,
> >>> 2 George Street, Brisbane, QLD 4000
> >>> Australia
> >>> LinkedIn
> >>> Research Gate
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Research Gate
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Received on Thu Aug 18 2016 - 02:00:06 PDT
