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
>>
>
>
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Received on Thu Aug 18 2016 - 02:00:05 PDT
