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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>
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--
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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Received on Mon Aug 22 2016 - 02:30:02 PDT
