It worked, Thank you Carlos.
Amit
On Sat, Dec 12, 2020 at 12:15 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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_
*Please consider the environment before printing this email.*
The
information contained in this electronic message and any *attachments to
this message are intended for the exclusive use of addressee(s) and may
contain proprietary, confidential or privileged information. If you are not
the intended recipient, you should not disseminate, distribute **or copy
this e-mail. Please notify the
sender immediately and destroy all copies of
this message and any attachments.***
**
**WARNING***: The recipient should
check this email and any attachments for
the presence of viruses. JMI
accepts no liability for any damage caused by any
virus transmitted by this
email.*
_______________________________________________
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Received on Fri Dec 11 2020 - 12:30:03 PST
