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
Received on Mon Mar 11 2013 - 06:30:03 PDT
