Re: [AMBER] solid surface simulation in amber

From: Neha Gandhi <n.gandhiau.gmail.com>
Date: Thu, 18 Aug 2016 18:27:28 +1000

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
>
-- 
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Thu Aug 18 2016 - 01:30:02 PDT
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