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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Received on Fri Oct 25 2013 - 11:30:02 PDT
