it looks like you load your original molecule as unit x, then save a pdb,
then load that back into unit x, which will overwrite your previous
information and you lose the box info etc.
try skipping those steps - create your unit x, do your bond/solvation etc,
then saveamberparm without overwriting the system by loading a pdb into the
same unit.
On Fri, Dec 11, 2020 at 1:21 PM Amit Sharma (Asstt. Prof., MCARS) <
asharma4.jmi.ac.in> wrote:
> command for solvation is as follows
>
> "
> solvateoct x OPCBOX 8.0
> 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
> Volume: 209323.503 A^3 (oct)
> Total mass 109655.332 amu, Density 0.870 g/cc
> Added 4991 residues.
> > savepdb x lov_wation.pdb
> Writing pdb file: lov_wation.pdb
> printing CRYST1 record to PDB file with box info
>
> Warning: Converting N-terminal residue name to PDB format: NPHE -> PHE
>
> Warning: Converting C-terminal residue name to PDB format: CLEU -> LEU
> > x = loadpdb lov_wation.pdb
> Loading PDB file: ./lov_wation.pdb
> total atoms in file: 22919
> > check x
> Checking 'x'....
>
> Warning: The unperturbed charge of the unit (0.155103) is not integral.
>
> Warning: The unperturbed charge of the unit (0.155103) is not zero.
> "
>
> I hope this provides the information.
>
> I attach a leap log file separately to you, as it may not go through the
> amber mailing list.
>
> Amit
>
>
>
> On Fri, Dec 11, 2020 at 10:43 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > it's hard to track what you're doing when we can't see your entire input
> > file.
> > however, from this new section it looks like you load a PDB file into
> unit
> > X, then save that molecule into a parm and rst7 file. there is no command
> > about solvation or a box, so I would not expect one to be present in
> those
> > files.
> >
> > On Fri, Dec 11, 2020 at 11:27 AM Amit Sharma (Asstt. Prof., MCARS) <
> > asharma4.jmi.ac.in> wrote:
> >
> > > Please see the part of leap log about the saved files
> > >
> > > >savepdb x lov_wation.pdb
> > > Writing pdb file: lov_wation.pdb
> > > printing CRYST1 record to PDB file with box info
> > >
> > > Warning: Converting N-terminal residue name to PDB format: NPHE -> PHE
> > >
> > > Warning: Converting C-terminal residue name to PDB format: CLEU -> LEU
> > > > x = loadpdb lov_wation.pdb
> > > Loading PDB file: ./lov_wation.pdb
> > > total atoms in file: 22919
> > > > saveamberparm x lov_wation.prmtop lov_wation.rst7
> > > Checking Unit.
> > >
> > > Warning: The unperturbed charge of the unit (0.155103) is not integral.
> > >
> > > Warning: The unperturbed charge of the unit (0.155103) is not zero.
> > >
> > > Note: Ignoring the error and warnings from Unit Checking.
> > >
> > > Building topology.
> > > Building atom parameters.
> > > Building bond parameters.
> > > Building angle parameters.
> > > Building proper torsion parameters.
> > > Building improper torsion parameters.
> > > total 480 improper torsions applied
> > > Building H-Bond parameters.
> > > Incorporating Non-Bonded adjustments.
> > > Not Marking per-residue atom chain types.
> > > Marking per-residue atom chain types.
> > > (Residues lacking connect0/connect1 -
> > > these don't have chain types marked:
> > >
> > > res total affected
> > >
> > > CLEU 1
> > > FMC 1
> > > NPHE 1
> > > WAT 5130
> > > )
> > > (no restraints)
> > >
> > > Amit
> > >
> > > On Fri, Dec 11, 2020 at 9:40 PM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > I'm still not seeing the part where you save your files. To be any
> > help I
> > > > need to see the leap inputs. Perhaps others can help out with the
> info
> > > that
> > > > you've provided though.
> > > >
> > > > On Fri, Dec 11, 2020 at 11:01 AM Amit Sharma (Asstt. Prof., MCARS) <
> > > > asharma4.jmi.ac.in> wrote:
> > > >
> > > > > last four lines of rst7 are as follows:
> > > > >
> > > > > "4.4530000 -1.4530000 -33.5420000 7.4510000 -4.4900000
> > > -37.0780000
> > > > > 6.6460000 -4.6000000 -36.7610000 7.3220000 -4.3890000
> > > -37.9350000
> > > > > 7.3130000 -4.4920000 -37.1570000 2.0370000 -1.4170000
> > > -35.4280000
> > > > > 2.5810000 -1.7580000 -34.8380000 2.0900000 -0.5590000
> > > -35.2860000
> > > > > 2.1260000 -1.3420000 -35.3200000"
> > > > >
> > > > >
> > > > > and the starting input lines from leap are as follows:
> > > > >
> > > > > "Welcome to LEaP!
> > > > > (no leaprc in search path)
> > > > > > source leaprc.protein.ff14SBonlysc
> > > > > ----- Source:
> > > > >
> > > > >
> > > >
> > >
> >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.protein.ff14SBonlysc
> > > > > ----- Source of
> > > > >
> > > > >
> > > >
> > >
> >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.protein.ff14SBonlysc
> > > > > done
> > > > > Log file: ./leap.log
> > > > > Loading parameters:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/parm10.dat
> > > > > Reading title:
> > > > > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > > > > Loading parameters:
> > > > >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/frcmod.ff14SB
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > ff14SB protein backbone and sidechain parameters
> > > > > Loading parameters:
> > > > >
> > /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/frcmod.ff99SB14
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > ff99SB backbone parameters (Hornak & Simmerling) with ff14SB atom
> > types
> > > > > Loading library:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/lib/amino12.lib
> > > > > Loading library:
> > > > >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/lib/aminoct12.lib
> > > > > Loading library:
> > > > >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/lib/aminont12.lib
> > > > > > source leaprc.gaff2
> > > > > ----- Source:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.gaff2
> > > > > ----- Source of
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.gaff2
> > > done
> > > > > Log file: ./leap.log
> > > > > Loading parameters:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/gaff2.dat
> > > > > Reading title:
> > > > > AMBER General Force Field for organic molecules (Version 2.11, May
> > > 2016)
> > > > > > source leaprc.water.opc
> > > > > ----- Source:
> > > > >
> > /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.water.opc
> > > > > ----- Source of
> > > > >
> > /home/amit/Amber20_complete/tools/amber20/dat/leap/cmd/leaprc.water.opc
> > > > > done
> > > > > Loading library:
> > > > >
> > /home/amit/Amber20_complete/tools/amber20/dat/leap/lib/atomic_ions.lib
> > > > > Loading library:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/lib/solvents.lib
> > > > > Loading parameters:
> > > > > /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/frcmod.opc
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863–3871)
> > > > > Loading parameters:
> > > > >
> > > > >
> > > >
> > >
> >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/frcmod.ionsjc_tip4pew
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > Monovalent ion parameters for Ewald and TIP4P/EW water from Joung &
> > > > > Cheatham JPCB (2008)
> > > > > Loading parameters:
> > > > >
> > > > >
> > > >
> > >
> >
> /home/amit/Amber20_complete/tools/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW
> > > water
> > > > > model (12-6 normal usage set)
> > > > > > loadAmberParams FMC.frcmod
> > > > > Loading parameters: ./FMC.frcmod
> > > > > Reading force field modification type file (frcmod)
> > > > > Reading title:
> > > > > this was copied from FMCcys but then edited to make the protein
> part
> > > (CB,
> > > > > SG etc) match ff14SB CYX atom types (c3, ss to 2C, S) since that's
> > what
> > > > > will bond to this residue. note that c3 showed up more than just
> the
> > CB
> > > > > atom
> > > > > > loadoff FMC.lib
> > > > > Loading library: ./FMC.lib"
> > > > >
> > > > > As you see there is no box info, I added the following box info at
> > the
> > > > last
> > > > > line from the pdb
> > > > > 67.7859143 67.7859143 67.7859143 109.4712190 109.4712190
> > > 109.471219
> > > > >
> > > > > and now i have set a minimization run through sander with following
> > > input
> > > > >
> > > > > &cntrl
> > > > > imin = 1,
> > > > > maxcyc = 100000,
> > > > > ncyc = 50000,
> > > > > ntb = 0, ! no periodicity
> > > > > cut = 99, ! non bond cut off
> > > > > ntr = 1,
> > > > > restraintmask= ':1 - 145 & !(.H=) &!(:CYX|:FMC=)',
> > > > > restraint_wt=100.0,
> > > > > /
> > > > >
> > > > >
> > > > >
> > > > > Amit
> > > > >
> > > > >
> > > > > On Fri, Dec 11, 2020 at 9:01 PM Carlos Simmerling <
> > > > > carlos.simmerling.gmail.com> wrote:
> > > > >
> > > > > > 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 - 11:00:02 PST
