Thank you so much! I have been messing with this for a while now and that
was a really simple fix.
Nicole
On Fri, Oct 25, 2013 at 3:06 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Assuming you built the residues OCS and FMR with GAFF, you need to add
> this command to the beginning of your leap input in order to load GAFF
> parameters:
>
> source leaprc.gaff
>
> -Dan
>
>
> On Fri, Oct 25, 2013 at 12:00 PM, Nicole Ippolito
> <ippolito.nicole89.gmail.com> wrote:
> > Hello,
> >
> > I am trying to run a constant pH simulation with 2 substrates inside my
> > enzyme. I am getting an error in the setup.
> >
> > My tleap.in file is the following:
> >>
> >> source leaprc.constph
> >> #loadparameters for FMR and OCS
> >> loadamberparams FMR.frcmod
> >> loadamberparams OCS.frcmod
> >> #load library
> >> loadoff FMR.lib
> >> loadoff OCS.lib
> >> # Load the PDBs
> >> FMR_OCS_mon = loadPDB Monoxygenase_2.pdb
> >> # Save topology files
> >> saveAmberParm FMR_OCS_mon FMR_OCS_mon.parm7 FMR_OCS_mon.rst7
> >> # Quit
> >> quit
> >>
> >> The following error is being generated when I run tleap with my
> tleap.infile
> >
> > -I: Adding /cm/shared/apps/amber12/dat/leap/prep to search path.
> > -I: Adding /cm/shared/apps/amber12/dat/leap/lib to search path.
> > -I: Adding /cm/shared/apps/amber12/dat/leap/parm to search path.
> > -I: Adding /cm/shared/apps/amber12/dat/leap/cmd to search path.
> > -f: Source tleap.in.
> >
> > Welcome to LEaP!
> > (no leaprc in search path)
> > Sourcing: ./tleap.in
> > ----- Source: /cm/shared/apps/amber12/dat/leap/cmd/leaprc.constph
> > ----- Source of /cm/shared/apps/amber12/dat/leap/cmd/leaprc.constph done
> > ----- Source: /cm/shared/apps/amber12/dat/leap/cmd/leaprc.ff10
> > ----- Source of /cm/shared/apps/amber12/dat/leap/cmd/leaprc.ff10 done
> > Log file: ./leap.log
> > Loading parameters: /cm/shared/apps/amber12/dat/leap/parm/parm10.dat
> > Reading title:
> > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/amino10.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/aminoct10.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/aminont10.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/phosphoaa10.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/nucleic10.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/ions08.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/solvents.lib
> > Loading library: /cm/shared/apps/amber12/dat/leap/lib/constph.lib
> > Loading library:
> /cm/shared/apps/amber12/dat/leap/lib/all_prot_nucleic10.lib
> > Loading library:
> /cm/shared/apps/amber12/dat/leap/lib/cph_nucleic_caps.lib
> > Loading parameters: /cm/shared/apps/amber12/dat/leap/parm/frcmod.constph
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Force field modifcations for titrations
> > Loading parameters:
> > /cm/shared/apps/amber12/dat/leap/parm/frcmod.protonated_nucleic
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Force field modifications for protonated nucleic acids
> > Using H(N)-modified Bondi radii
> > Loading parameters: ./FMR.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > remark goes here
> > Loading parameters: ./OCS.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > remark goes here
> > Loading library: ./FMR.lib
> > Loading library: ./OCS.lib
> > Loading PDB file: ./Monoxygenase_2.pdb
> > total atoms in file: 2877
> > Leap added 2769 missing atoms according to residue templates:
> > 2769 H / lone pairs
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: 0.999998 is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<FMR 362>.A<N1 1> Could not find type: na
> > For atom: .R<FMR 362>.A<C1 2> Could not find type: c3
> > For atom: .R<FMR 362>.A<C2 3> Could not find type: cc
> > For atom: .R<FMR 362>.A<C3 4> Could not find type: ca
> > For atom: .R<FMR 362>.A<C4 5> Could not find type: c3
> > For atom: .R<FMR 362>.A<H1 6> Could not find type: h1
> > For atom: .R<FMR 362>.A<H2 7> Could not find type: h1
> > For atom: .R<FMR 362>.A<C5 8> Could not find type: c3
> > For atom: .R<FMR 362>.A<C6 9> Could not find type: c3
> > For atom: .R<FMR 362>.A<C7 10> Could not find type: c3
> > For atom: .R<FMR 362>.A<O1 11> Could not find type: os
> > For atom: .R<FMR 362>.A<H3 12> Could not find type: h1
> > For atom: .R<FMR 362>.A<H4 13> Could not find type: h1
> > For atom: .R<FMR 362>.A<P1 14> Could not find type: p5
> > For atom: .R<FMR 362>.A<O2 15> Could not find type: o
> > For atom: .R<FMR 362>.A<O3 16> Could not find type: o
> > For atom: .R<FMR 362>.A<O4 17> Could not find type: o
> > For atom: .R<FMR 362>.A<N2 18> Could not find type: n
> > For atom: .R<FMR 362>.A<C8 19> Could not find type: cd
> > For atom: .R<FMR 362>.A<C9 20> Could not find type: c
> > For atom: .R<FMR 362>.A<H5 21> Could not find type: hn
> > For atom: .R<FMR 362>.A<N3 22> Could not find type: n
> > For atom: .R<FMR 362>.A<O5 23> Could not find type: o
> > For atom: .R<FMR 362>.A<C10 24> Could not find type: c
> > For atom: .R<FMR 362>.A<H6 25> Could not find type: hn
> > For atom: .R<FMR 362>.A<O6 26> Could not find type: o
> > For atom: .R<FMR 362>.A<N4 27> Could not find type: na
> > For atom: .R<FMR 362>.A<C11 28> Could not find type: ca
> > For atom: .R<FMR 362>.A<H7 29> Could not find type: hn
> > For atom: .R<FMR 362>.A<C12 30> Could not find type: ca
> > For atom: .R<FMR 362>.A<C13 31> Could not find type: ca
> > For atom: .R<FMR 362>.A<C14 32> Could not find type: ca
> > For atom: .R<FMR 362>.A<H8 33> Could not find type: ha
> > For atom: .R<FMR 362>.A<C15 34> Could not find type: c3
> > For atom: .R<FMR 362>.A<C16 35> Could not find type: ca
> > For atom: .R<FMR 362>.A<H9 36> Could not find type: hc
> > For atom: .R<FMR 362>.A<H10 37> Could not find type: hc
> > For atom: .R<FMR 362>.A<H11 38> Could not find type: hc
> > For atom: .R<FMR 362>.A<C17 39> Could not find type: c3
> > For atom: .R<FMR 362>.A<H12 40> Could not find type: hc
> > For atom: .R<FMR 362>.A<H13 41> Could not find type: hc
> > For atom: .R<FMR 362>.A<H14 42> Could not find type: hc
> > For atom: .R<FMR 362>.A<H15 43> Could not find type: ha
> > For atom: .R<FMR 362>.A<H16 44> Could not find type: h1
> > For atom: .R<FMR 362>.A<H17 45> Could not find type: h1
> > For atom: .R<FMR 362>.A<H18 46> Could not find type: h1
> > For atom: .R<FMR 362>.A<O7 47> Could not find type: oh
> > For atom: .R<FMR 362>.A<H19 48> Could not find type: ho
> > For atom: .R<FMR 362>.A<O8 49> Could not find type: oh
> > For atom: .R<FMR 362>.A<H20 50> Could not find type: ho
> > For atom: .R<FMR 362>.A<O9 51> Could not find type: oh
> > For atom: .R<FMR 362>.A<H21 52> Could not find type: ho
> > For atom: .R<OCS 363>.A<C1 1> Could not find type: c3
> > For atom: .R<OCS 363>.A<C2 2> Could not find type: c3
> > For atom: .R<OCS 363>.A<C3 3> Could not find type: c3
> > For atom: .R<OCS 363>.A<H1 4> Could not find type: hc
> > For atom: .R<OCS 363>.A<H2 5> Could not find type: hc
> > For atom: .R<OCS 363>.A<C4 6> Could not find type: c3
> > For atom: .R<OCS 363>.A<H3 7> Could not find type: hc
> > For atom: .R<OCS 363>.A<H4 8> Could not find type: hc
> > For atom: .R<OCS 363>.A<C5 9> Could not find type: c3
> > For atom: .R<OCS 363>.A<H5 10> Could not find type: hc
> > For atom: .R<OCS 363>.A<H6 11> Could not find type: hc
> > For atom: .R<OCS 363>.A<H7 12> Could not find type: hc
> > For atom: .R<OCS 363>.A<H8 13> Could not find type: hc
> > For atom: .R<OCS 363>.A<H9 14> Could not find type: hc
> > For atom: .R<OCS 363>.A<C6 15> Could not find type: c3
> > For atom: .R<OCS 363>.A<H10 16> Could not find type: hc
> > For atom: .R<OCS 363>.A<H11 17> Could not find type: hc
> > For atom: .R<OCS 363>.A<C7 18> Could not find type: c3
> > For atom: .R<OCS 363>.A<H12 19> Could not find type: hc
> > For atom: .R<OCS 363>.A<H13 20> Could not find type: hc
> > For atom: .R<OCS 363>.A<C8 21> Could not find type: c3
> > For atom: .R<OCS 363>.A<H14 22> Could not find type: hc
> > For atom: .R<OCS 363>.A<H15 23> Could not find type: hc
> > For atom: .R<OCS 363>.A<S1 24> Could not find type: s6
> > For atom: .R<OCS 363>.A<H16 25> Could not find type: h1
> > For atom: .R<OCS 363>.A<H17 26> Could not find type: h1
> > For atom: .R<OCS 363>.A<O1 27> Could not find type: o
> > For atom: .R<OCS 363>.A<O2 28> Could not find type: o
> > For atom: .R<OCS 363>.A<O3 29> Could not find type: o
> > Parameter file was not saved.
> > Quit
> >
> >
> >
> > I am unsure how to fix this and help would be greatly appreciated.
> >
> > Thank you,
> >
> > Nicole Ippolito
> > Auburn University
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 25 2013 - 15:00:03 PDT
