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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
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Received on Fri Aug 19 2016 - 18:30:02 PDT
