> When I used the interface ff parameters, I still get high restraint
energies.
> ... Are these non-bonded parameters making my system unstable?
If they are causing your restraint energies to be high, I'd expect the
vdw term to also be high - is it?
You could try relaxing the restraints, and see what it does to the geometry.
Bill
On 8/22/16 2:00 AM, Neha Gandhi wrote:
> I would refrain talking about supercell and only talk about unit cell in
> this post. As Bill Ross suggested, I have now 3 residues CAP for calcium,
> OAP for OH and PAP for phosphate.
>
> I took unit cell parameters from the interface force-field developers and
> used their coordinates. I also used vmd to get box dimensions. The box size
> shown by vmd is equal to the that reported in the unit cell.
>
> I just tried using gaff parameters to see if the restraints work. When I
> visualized the minimization trajectory, the HAP molecules doesn't show
> distorted geometry nor a high displacement, this is what I expected to see
> (to apply position restraints on HAP).
>
> When I used the interface ff parameters, I still get high restraint
> energies. The force-field developers have increase the non-bonded
> parameters for phosphate and calcium as below.
>
> NG 3.30 0.130 (calcium)
> PP 4.30 0.280 (P in the phosphate)
> OP 3.40 0.070 (O in the phosphate)
>
> Are these non-bonded parameters making my system unstable?
>
> Regards,
> Neha
>
>
>
>
> On 20 August 2016 at 11:35, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> If they aren't bonded to other atoms, yes.
>>
>> Bill
>>
>>
>> On 8/19/16 6:28 PM, Neha Gandhi wrote:
>>> Does that mean I m better off defining phosphate, calcium and OH as
>>> individual residues?
>>>
>>> On 20 Aug 2016 7:06 AM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>>>
>>>> Looking at ambpdb's rendition of Neha's inpcrd, prmtop, to my mind there
>>>> should not be TER cards within a residue. The basic problem might be
>>>> trying to express everything as one residue. I'm not up-to-date enough
>>>> to guess exactly why ambpdb is putting TERs in there, but it seems like
>>>> a problem to me. Two snippets below to illustrate.
>>>>
>>>> Bill
>>>>
>>>> CRYST1 43.924 52.874 40.136 90.00 90.00 90.00 1
>>>> ATOM 1 O11 HAP 1 17.911 21.033 17.113 1.00
>>>> 0.00 O
>>>> ATOM 2 O12 HAP 1 17.911 21.033 19.584 1.00
>>>> 0.00 O
>>>> ATOM 3 P1 HAP 1 18.693 21.483 18.349 1.00
>>>> 0.00 P
>>>> ATOM 4 O13 HAP 1 18.713 23.020 18.349 1.00
>>>> 0.00 O
>>>> ATOM 5 O14 HAP 1 20.118 20.914 18.349 1.00
>>>> 0.00 O
>>>> TER 6 HAP 1
>>>> ATOM 6 O21 HAP 1 18.975 25.690 17.113 1.00
>>>> 0.00 O
>>>> ATOM 7 O22 HAP 1 18.975 25.690 19.584 1.00
>>>> 0.00 O
>>>> ATOM 8 P2 HAP 1 18.195 26.142 18.349 1.00
>>>> 0.00 P
>>>> ATOM 9 O23 HAP 1 16.854 25.391 18.349 1.00
>>>> 0.00 O
>>>> ATOM 10 O24 HAP 1 17.975 27.660 18.349 1.00
>>>> 0.00 O
>>>>
>>>> And later:
>>>>
>>>> ATOM 39 CA19 HAP 1 18.293 20.193 21.786 1.00
>>>> 0.00 CA
>>>> TER 40 HAP 1
>>>> ATOM 40 CA20 HAP 1 24.220 18.286 21.786 1.00
>>>> 0.00 CA
>>>> TER 41 HAP 1
>>>> ATOM 41 O1 HAP 1 17.099 18.232 22.144 1.00
>>>> 0.00 O
>>>> ATOM 42 H1 HAP 1 17.099 18.232 23.254 1.00
>>>> 0.00 H
>>>> TER 43 HAP 1
>>>> ATOM 43 O71 HAP 1 22.620 29.189 17.113 1.00
>>>> 0.00 O
>>>> ATOM 44 O72 HAP 1 22.620 29.189 19.584 1.00
>>>> 0.00 O
>>>> ATOM 45 P7 HAP 1 23.402 29.639 18.349 1.00
>>>> 0.00 P
>>>>
>>>>
>>>>
>>>> On 8/19/16 1:57 AM, Neha Gandhi wrote:
>>>>> I am adding further details (see the trail of emails below)
>>>>>
>>>>> Instead of minimizing supercell, I tried to look at unit cell and check
>>>> the
>>>>> minimzation.
>>>>>
>>>>> The unit cell dimensions are correct (I checked in vmd, materials
>> studio,
>>>>> and also tried setBox m1 centers/vdw)
>>>>> I also tried increasing the box size in each dimension by 1 A.
>>>>>
>>>>> As Bill suggested, I tried visualising the trajectory of initial
>>>> structure
>>>>> versus minimzation rst file. It seems although I am holding the HAP
>> atoms
>>>>> fixed (ntr=1, restraint weight >> 500) in the cell, the atoms are
>> moving
>>>>> and affects the geometry.
>>>>>
>>>>> .Bill: I also tried fixatomorder in case the inpcrd has some issues,
>> but
>>>> it
>>>>> didn't make any difference to my results. When I output the min.rst as
>>>> pdb,
>>>>> it has correct elements in the last column.
>>>>>
>>>>> How do I work around this problem? How to fix HAP surface?
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 18 August 2016 at 23:13, David A Case <david.case.rutgers.edu>
>> wrote:
>>>>>> On Thu, Aug 18, 2016, Neha Gandhi wrote:
>>>>>>> I have a pdb file of a unit cell and I am converting using
>> antechamber
>>>> to
>>>>>>> mol2 file
>>>>>> It sounds like the problem might be right here: how did you get this
>>>> file?
>>>>>> Are you sure that the unit cell parameters (in the CRYST1 line) are
>>>>>> correct?
>>>>>>
>>>>>>> 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}
>>>>>> The "supercell.pdb" file should already
>>>>>> have the proper Unit Cell values. Are they different than {145 150
>> 39}?
>>>>>>> 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 agree that this is very odd, given the huge vdW energy on the first
>>>> step
>>>>>> of minimization.
>>>>>>
>>>>>>> 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 ...
>>>>>> Can you say what it is about the PDB file that led you the think that
>>>> the
>>>>>> calcium ion is interpreted as carbon? PDB files have the element at
>> the
>>>>>> far
>>>>>> right of the ATOM card...what does that show?
>>>>>>
>>>>>> ....dac
>>>>>>
>>>>>>
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Received on Mon Aug 22 2016 - 03:30:02 PDT
