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
> > > >
> > > > --
> > > > _
> > > > _
> > > >
> > > >
> > > >
> > > > *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.*
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > --
> > _
> > _
> >
> >
> >
> > *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.*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_
_
*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.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 11 2020 - 08:30:02 PST
