Re: [AMBER] Constant pH with enzyme and substrate

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 25 Oct 2013 14:06:23 -0600

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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> 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
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