I don't see anything unusual, maybe others do... but it's hard to know
without seeing your actual leap input.
perhaps you could also show the last few lines of the rst7 produced by leap.
On Fri, Dec 11, 2020 at 9:53 AM Amit Sharma (Asstt. Prof., MCARS) <
asharma4.jmi.ac.in> wrote:
> My tleap input is as follows
>
> > source leaprc.protein.ff14SBonlysc
> > source leaprc.gaff2
> Joung-Chetham monovalent ions for> source leaprc.water.opc
> This gives (nothing unusual)
>
>
>
> > loadAmberParams FMC.frcmod
> > loadoff FMC.lib
> > x = loadpdb protein.pdb (where protein.pdb is protein containing FMC
> (FMN))
> > solvateoct x OPCBOX 8.0
> This gives
> "Scaling up box by a factor of 1.309835 to meet diagonal cut criterion
> Solute vdw bounding box: 52.851 41.765 42.392
> Total bounding box for atom centers: 73.808 73.808 73.808
> (box expansion for 'iso' is 37.1%)
> Solvent unit box: 18.865 18.478 19.006
> The number of boxes: x= 4 y= 4 z= 4
> Volume: 209323.503 A^3 (oct)
> Total mass 109655.332 amu, Density 0.870 g/cc
> Added 4991 residues."
>
>
> and then on checking the molecule x gives non integral, non zero charge of
> -5.844897. This becomes +0.155103 after I add 6 Na+ ions.
>
> then I save rst7 and prmtop files. And, at this stage I do not get box info
> in rst7.
>
> Amit
>
>
>
>
>
>
>
> On Fri, Dec 11, 2020 at 7:01 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I suggest looking in your leap.log file to see what leap responded when
> you
> > asked to solvate the system. if you still have trouble, sharing that part
> > of the log file along with your leap input may make it easier for people
> to
> > help you debug.
> >
> > On Fri, Dec 11, 2020 at 8:14 AM Amit Sharma (Asstt. Prof., MCARS) <
> > asharma4.jmi.ac.in> wrote:
> >
> > > Hi,
> > >
> > > I solvated my protein+chromophore system in an OPC water model using 8
> > > Angstrom OPCBOX.
> > >
> > > But, last line of rst7 file does not contain box info. Hence, initial
> > > minimization (with ntb = 1) is not working. Although, the issue does
> not
> > > arise when using a tip3p water box (but, i need to use opc water).
> > >
> > > Then, I tried minimization after copying the box info from the pdb, but
> > > this aswell stops with the following out info
> > >
> > > "NFFT1 = 72 NFFT2 = 375 NFFT3 = 375
> > > Cutoff= 8.000 Tol =0.100E-04
> > > Ewald Coefficient = 0.34864
> > > Interpolation order = 4
> > >
> > > Ewald PARAMETER RANGE CHECKING:
> > > parameter alpha: (unit cell angle) has value 0.31095E+04
> > > This is outside the legal range
> > > Lower limit: 0.30000E+02 Upper limit: 0.15000E+03
> > > Check ew_legal.h"
> > >
> > > Any suggestions on how to resolve this issue?
> > >
> > > Thanks,
> > >
> > > Amit
> > >
> > > --
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Received on Fri Dec 11 2020 - 07:30:02 PST
