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
> _______________________________________________
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> 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)
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Received on Fri Oct 25 2013 - 13:30:08 PDT
