> I do not see any overlap/problem with any neighbouring atoms in the
starting structure.
If you generate a pdb from your inpcrd and run the overlap checker, you
might find something.
Another possibility based on min.rst first step is that you have somehow
mixed up your files, so the prmtop doesn't match the coordinates. I.e.
check your scripts closely.
I think you can save mdcrd for the min steps - it sounds like it would
be an interesting animation to watch, might give insight.
Bill
On 8/18/16 1:48 AM, Neha Gandhi wrote:
> 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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 18 2016 - 02:00:08 PDT
