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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>
--
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 Fri Aug 19 2016 - 02:00:02 PDT
