Re: [AMBER] generate prepin from mol2 which has charges/atom types for Heme from Vaibhav Dixit on 2013-03-10 (Amber Archive Mar 2013)

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 11 Mar 2013 10:07:45 +0530

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

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chemical/x-pdb attachment: 2VN0_heme2.pdb

application/octet-stream attachment: Heme.mol2

application/octet-stream attachment: Heme.frcmod

Received on Sun Mar 10 2013 - 22:00:02 PDT