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 - 07:00:03 PST
