Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 11 Mar 2013 20:54:57 +0530

Dear Jason and Amber people,
I have made necessary corrections in the leap_TGZ.in file (below). I have
deleted hydrogen from pdb which were causing problems and allowed tleap to
add them, is this sensible or I should remove all protein Hs? (new PDB is
attached). But after that new error related to the HEM N-Fe bond/atomtypes
are coming.
Please suggest how to add these new atom types to avoid this error. Thanks
for the vital suggestions.

leap_TGZ.in file:
--------
source leaprc.ff99SB
source leaprc.gaff
loadamberparams Heme.frcmod
HEM = loadmol2 Heme.mol2
2vn0 = loadpdb 2VN0_heme2.pdb

gm.linux-rfml:~/Documents/MD/CYP450/TGZ_2vn0> tleap -s -f leap_TGZ.in
-I: Adding /usr/local/amber12/dat/leap/prep to search path.
-I: Adding /usr/local/amber12/dat/leap/lib to search path.
-I: Adding /usr/local/amber12/dat/leap/parm to search path.
-I: Adding /usr/local/amber12/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap_TGZ.in.

Welcome to LEaP!
Sourcing: ./leap_TGZ.in
----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB
----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /usr/local/amber12/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /usr/local/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber12/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber12/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber12/dat/leap/lib/solvents.lib
----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010)
add. info. at the end
Loading parameters: ./Heme.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./Heme.mol2
Reading MOLECULE named HEM
Loading PDB file: ./2VN0_heme2.pdb
  Added missing heavy atom: .R<CHIE 491>.A<OXT 18>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NA-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-ND-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NC-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
  total atoms in file: 7491
  Leap added 12 missing atoms according to residue templates:
       1 Heavy
       11 H / lone pairs


On Mon, Mar 11, 2013 at 6:39 PM, Jason Swails <jason.swails.gmail.com>wrote:

> Your command in your tleap file that reads
>
> loadamberparms Heme.frcmod
>
> should be
>
> loadamberparams Heme.frcmod
>
> (You are missing an 'a' between the r and m). Admittedly the error message
> should be better (e.g., "loadamberparms command not found", or something).
>
> However, that is not the end of the problems. Even after that is fixed, I
> get the following errors when trying to save your topology file:
>
> > saveamberparm 2vn0 this.prmtop that.inpcrd
> Checking Unit.
> ERROR: The unperturbed charge of the unit: 4.402400 is not integral.
> WARNING: The unperturbed charge of the unit: 4.402400 is not zero.
> FATAL: Atom .R<HIE 150>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 230>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 251>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 316>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 329>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 353>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 368>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 396>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 411>.A<HD1 18> does not have a type.
> FATAL: Atom .R<GLU 444>.A<HE2 16> does not have a type.
> FATAL: Atom .R<CHIE 491>.A<HXT 19> does not have a type.
> FATAL: Atom .R<CHIE 491>.A<HD1 20> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> > quit
> Quit
>
> So I would check your input PDB carefully as well as the charge on your
> Heme group. This is what tleap tells me:
>
> > check HEM
> Checking 'HEM'....
> ERROR: The unperturbed charge of the unit: -1.597600 is not integral.
> WARNING: The unperturbed charge of the unit: -1.597600 is not zero.
> Checking parameters for unit 'HEM'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warnings: 1
>
> So the good news is that the mol2 file is not your problem. The bad news
> is that now you have other problems to fix...
>
> Good luck,
> Jason
>
> On Mon, Mar 11, 2013 at 12:37 AM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Dr. Jason, Prof. Case and Amber people,
> > Thanks for the clarification. I have used the following set of commands
> in
> > the leap_TGZ.in file, but there seems to be a syntax error while reading
> > the mol2 file. Please suggest on the source of this error and how to
> avoid
> > it so that I can load the parameters for heme properly.
> > The mol2, frcmod and P450 pdb that I am trying to run MD for are
> attached.
> > The protein structure was prepared using "protein preparation wizard" of
> > Schrodinger package.
> >
> > Another doubt: Will tleap use the Heme coordinates in the mol2 or the
> > protein pdb while generating prmtop and inpcrd? How to make sure that it
> > uses coordinates in the protein pdb?
> >
> > leap_TGZ.in file
> > --------
> > source leaprc.ff99SB
> > source leaprc.gaff
> > heme = loadmol2 Heme.mol2
> > loadamberparms Heme.frcmod
> > 2vn0 = loadpdb 2VN0_heme2.pdb
> >
> >
> > gm.linux-rfml:~/Documents/MD/CYP450/TGZ_2vn0> tleap -s -f leap_TGZ.in
> > -I: Adding /usr/local/amber12/dat/leap/prep to search path.
> > -I: Adding /usr/local/amber12/dat/leap/lib to search path.
> > -I: Adding /usr/local/amber12/dat/leap/parm to search path.
> > -I: Adding /usr/local/amber12/dat/leap/cmd to search path.
> > -s: Ignoring startup file: leaprc
> > -f: Source leap_TGZ.in.
> >
> > Welcome to LEaP!
> > Sourcing: ./leap_TGZ.in
> > ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB
> > ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.ff99SB done
> > Log file: ./leap.log
> > Loading parameters: /usr/local/amber12/dat/leap/parm/parm99.dat
> > Reading title:
> > PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> > incl.02/04/99
> > Loading parameters: /usr/local/amber12/dat/leap/parm/frcmod.ff99SB
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Modification/update of parm99.dat (Hornak & Simmerling)
> > Loading library: /usr/local/amber12/dat/leap/lib/all_nucleic94.lib
> > Loading library: /usr/local/amber12/dat/leap/lib/all_amino94.lib
> > Loading library: /usr/local/amber12/dat/leap/lib/all_aminoct94.lib
> > Loading library: /usr/local/amber12/dat/leap/lib/all_aminont94.lib
> > Loading library: /usr/local/amber12/dat/leap/lib/ions94.lib
> > Loading library: /usr/local/amber12/dat/leap/lib/solvents.lib
> > ----- Source: /usr/local/amber12/dat/leap/cmd/leaprc.gaff
> > ----- Source of /usr/local/amber12/dat/leap/cmd/leaprc.gaff done
> > Log file: ./leap.log
> > Loading parameters: /usr/local/amber12/dat/leap/parm/gaff.dat
> > Reading title:
> > AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> > add. info. at the end
> > Loading Mol2 file: ./Heme.mol2
> > Reading MOLECULE named HEM
> > *ERROR: syntax error*
> >
> > Loading PDB file: ./2VN0_heme2.pdb
> > Unknown residue: HEM number: 464 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Created a new atom named: HD1 within residue: .R<HIE 150>
> > Created a new atom named: HD1 within residue: .R<HIE 230>
> > Created a new atom named: HD1 within residue: .R<HIE 251>
> > Created a new atom named: HD1 within residue: .R<HIE 316>
> > Created a new atom named: HD1 within residue: .R<HIE 329>
> > Created a new atom named: HD1 within residue: .R<HIE 353>
> > Created a new atom named: HD1 within residue: .R<HIE 368>
> > Created a new atom named: HD1 within residue: .R<HIE 396>
> > Created a new atom named: HD1 within residue: .R<HIE 411>
> > Created a new atom named: HE2 within residue: .R<GLU 444>
> > Created a new atom named: HXT within residue: .R<CHIE 491>
> > Created a new atom named: HD1 within residue: .R<CHIE 491>
> > Added missing heavy atom: .R<CHIE 491>.A<OXT 18>
> > Creating new UNIT for residue: HEM sequence: 492
> > Created a new atom named: FE within residue: .R<HEM 492>
> > Created a new atom named: CHA within residue: .R<HEM 492>
> > Created a new atom named: CHB within residue: .R<HEM 492>
> > Created a new atom named: CHC within residue: .R<HEM 492>
> > Created a new atom named: CHD within residue: .R<HEM 492>
> > Created a new atom named: NA within residue: .R<HEM 492>
> > Created a new atom named: C1A within residue: .R<HEM 492>
> > Created a new atom named: C2A within residue: .R<HEM 492>
> > Created a new atom named: C3A within residue: .R<HEM 492>
> > Created a new atom named: C4A within residue: .R<HEM 492>
> > Created a new atom named: CMA within residue: .R<HEM 492>
> > Created a new atom named: CAA within residue: .R<HEM 492>
> > Created a new atom named: CBA within residue: .R<HEM 492>
> > Created a new atom named: CGA within residue: .R<HEM 492>
> > Created a new atom named: O1A within residue: .R<HEM 492>
> > Created a new atom named: O2A within residue: .R<HEM 492>
> > Created a new atom named: NB within residue: .R<HEM 492>
> > Created a new atom named: C1B within residue: .R<HEM 492>
> > Created a new atom named: C2B within residue: .R<HEM 492>
> > Created a new atom named: C3B within residue: .R<HEM 492>
> > Created a new atom named: C4B within residue: .R<HEM 492>
> > Created a new atom named: CMB within residue: .R<HEM 492>
> > Created a new atom named: CAB within residue: .R<HEM 492>
> > Created a new atom named: CBB within residue: .R<HEM 492>
> > Created a new atom named: NC within residue: .R<HEM 492>
> > Created a new atom named: C1C within residue: .R<HEM 492>
> > Created a new atom named: C2C within residue: .R<HEM 492>
> > Created a new atom named: C3C within residue: .R<HEM 492>
> > Created a new atom named: C4C within residue: .R<HEM 492>
> > Created a new atom named: CMC within residue: .R<HEM 492>
> > Created a new atom named: CAC within residue: .R<HEM 492>
> > Created a new atom named: CBC within residue: .R<HEM 492>
> > Created a new atom named: C1D within residue: .R<HEM 492>
> > Created a new atom named: C2D within residue: .R<HEM 492>
> > Created a new atom named: C3D within residue: .R<HEM 492>
> > Created a new atom named: C4D within residue: .R<HEM 492>
> > Created a new atom named: CMD within residue: .R<HEM 492>
> > Created a new atom named: CAD within residue: .R<HEM 492>
> > Created a new atom named: CBD within residue: .R<HEM 492>
> > Created a new atom named: CGD within residue: .R<HEM 492>
> > Created a new atom named: O1D within residue: .R<HEM 492>
> > Created a new atom named: O2D within residue: .R<HEM 492>
> > Created a new atom named: ND within residue: .R<HEM 492>
> > Created a new atom named: HHA within residue: .R<HEM 492>
> > Created a new atom named: HHB within residue: .R<HEM 492>
> > Created a new atom named: HHC within residue: .R<HEM 492>
> > Created a new atom named: HHD within residue: .R<HEM 492>
> > Created a new atom named: HMA1 within residue: .R<HEM 492>
> > Created a new atom named: HMA2 within residue: .R<HEM 492>
> > Created a new atom named: HMA3 within residue: .R<HEM 492>
> > Created a new atom named: HAA1 within residue: .R<HEM 492>
> > Created a new atom named: HAA2 within residue: .R<HEM 492>
> > Created a new atom named: HBA1 within residue: .R<HEM 492>
> > Created a new atom named: HBA2 within residue: .R<HEM 492>
> > Created a new atom named: HMB1 within residue: .R<HEM 492>
> > Created a new atom named: HMB2 within residue: .R<HEM 492>
> > Created a new atom named: HMB3 within residue: .R<HEM 492>
> > Created a new atom named: HAB within residue: .R<HEM 492>
> > Created a new atom named: HBB1 within residue: .R<HEM 492>
> > Created a new atom named: HBB2 within residue: .R<HEM 492>
> > Created a new atom named: HMC1 within residue: .R<HEM 492>
> > Created a new atom named: HMC2 within residue: .R<HEM 492>
> > Created a new atom named: HMC3 within residue: .R<HEM 492>
> > Created a new atom named: HAC within residue: .R<HEM 492>
> > Created a new atom named: HBC1 within residue: .R<HEM 492>
> > Created a new atom named: HBC2 within residue: .R<HEM 492>
> > Created a new atom named: HMD1 within residue: .R<HEM 492>
> > Created a new atom named: HMD2 within residue: .R<HEM 492>
> > Created a new atom named: HMD3 within residue: .R<HEM 492>
> > Created a new atom named: HAD1 within residue: .R<HEM 492>
> > Created a new atom named: HAD2 within residue: .R<HEM 492>
> > Created a new atom named: HBD1 within residue: .R<HEM 492>
> > Created a new atom named: HBD2 within residue: .R<HEM 492>
> > total atoms in file: 7505
> > Leap added 10 missing atoms according to residue templates:
> > 1 Heavy
> > 9 H / lone pairs
> > The file contained 85 atoms not in residue templates
> > >
> >
> >
> >
> >
> > On Sun, Mar 10, 2013 at 9:54 PM, David A Case <case.biomaps.rutgers.edu
> > >wrote:
> >
> > > On Sun, Mar 10, 2013, Vaibhav Dixit wrote:
> > >
> > > > Authors have given mol2 and frcmod for Heme (in supporting info). But
> > to
> > > > generate suitable prmtop and inpcrd files we need both prepin and
> > frcmod
> > > > files.
> > >
> > > This is not correct: LEaP can real mol2 files as well as prepin files,
> > so a
> > > combination of mol2 and frcmod should in principle be all you need.
> > >
> > > ...dac
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D.
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408, +91-7709129400.
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in



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Received on Mon Mar 11 2013 - 08:30:03 PDT
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