Hi Bill,
I used a restraint weight of 1 kcal/molecular/A but still it distorts the
geometry. The authors have reparameterised non bonded terms to fit solid
surfaces. However they ran their simulations in materials studio and not
Amber.
On 22 Aug 2016 8:08 PM, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
> > 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
