Dear list,
I am new to Amber so excuse me if my questions are rather basic. I try to prepare the topology files for using it later in NAMD. I was reading the previous listing: http://archive.ambermd.org/201010/0304.html to prepare the files necessary.
I stripped from the PDB (3EKD) file all water molecules and CONECT entries in addition to the ligand coordinates (not the heme). This leaves me with the two chains of my P450 and the two hemes in the PDB file. I modified the all atoms heme parameter files like mentioned in above's listing. The problem is that I get error messages about the torsion angles in the heme. Are these only warnings? If not how can I fix that? What is exactly the problem?
mber12/bin/tleap -f leaprc.ff99SB
-I: Adding /Users/doom4/Downloads/amber12/dat/leap/prep to search path.
-I: Adding /Users/doom4/Downloads/amber12/dat/leap/lib to search path.
-I: Adding /Users/doom4/Downloads/amber12/dat/leap/parm to search path.
-I: Adding /Users/doom4/Downloads/amber12/dat/leap/cmd to search path.
-f: Source leaprc.ff99SB.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Users/doom4/Downloads/amber12/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /Users/doom4/Downloads/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: /Users/doom4/Downloads/amber12/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/all_nucleic94.lib
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/all_amino94.lib
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/all_aminoct94.lib
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/all_aminont94.lib
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/ions94.lib
Loading library: /Users/doom4/Downloads/amber12/dat/leap/lib/solvents.lib
> loadamberparams frcmod.hemall.txt
Loading parameters: ./frcmod.hemall.txt
Reading force field modification type file (frcmod)
Reading title:
> loadamberprep heme_all.in.txt
Loading Prep file: ./heme_all.in.txt
(no charges read on atoms lines in Heme residue ALL ATOM, Yves names, Bayly-modified)
> cyp = loadpdb 3EKD.pdb
Loading PDB file: ./3EKD.pdb
(starting new molecule for chain B)
Added missing heavy atom: .R<GLU 4>.A<CG 8>
Added missing heavy atom: .R<GLU 4>.A<CD 11>
Added missing heavy atom: .R<GLU 4>.A<OE1 12>
Added missing heavy atom: .R<GLU 4>.A<OE2 13>
Added missing heavy atom: .R<LYS 31>.A<CE 14>
Added missing heavy atom: .R<LYS 31>.A<NZ 17>
Added missing heavy atom: .R<LYS 94>.A<CE 14>
Added missing heavy atom: .R<LYS 94>.A<NZ 17>
Added missing heavy atom: .R<GLN 109>.A<CG 8>
Added missing heavy atom: .R<GLN 109>.A<CD 11>
Added missing heavy atom: .R<GLN 109>.A<OE1 12>
Added missing heavy atom: .R<GLN 109>.A<NE2 13>
Added missing heavy atom: .R<GLN 110>.A<CD 11>
Added missing heavy atom: .R<GLN 110>.A<OE1 12>
Added missing heavy atom: .R<GLN 110>.A<NE2 13>
Added missing heavy atom: .R<LYS 113>.A<CD 11>
Added missing heavy atom: .R<LYS 113>.A<CE 14>
Added missing heavy atom: .R<LYS 113>.A<NZ 17>
Added missing heavy atom: .R<ASN 192>.A<CG 8>
Added missing heavy atom: .R<ASN 192>.A<OD1 9>
Added missing heavy atom: .R<ASN 192>.A<ND2 10>
Added missing heavy atom: .R<LYS 210>.A<CE 14>
Added missing heavy atom: .R<LYS 210>.A<NZ 17>
Added missing heavy atom: .R<LYS 218>.A<CG 8>
Added missing heavy atom: .R<LYS 218>.A<CD 11>
Added missing heavy atom: .R<LYS 218>.A<CE 14>
Added missing heavy atom: .R<LYS 218>.A<NZ 17>
Added missing heavy atom: .R<LYS 224>.A<CD 11>
Added missing heavy atom: .R<LYS 224>.A<CE 14>
Added missing heavy atom: .R<LYS 224>.A<NZ 17>
Added missing heavy atom: .R<GLN 285>.A<CD 11>
Added missing heavy atom: .R<GLN 285>.A<OE1 12>
Added missing heavy atom: .R<GLN 285>.A<NE2 13>
Added missing heavy atom: .R<LYS 303>.A<CD 11>
Added missing heavy atom: .R<LYS 303>.A<CE 14>
Added missing heavy atom: .R<LYS 303>.A<NZ 17>
Added missing heavy atom: .R<CGLY 454>.A<OXT 8>
Added missing heavy atom: .R<LYS 456>.A<CD 11>
Added missing heavy atom: .R<LYS 456>.A<CE 14>
Added missing heavy atom: .R<LYS 456>.A<NZ 17>
Added missing heavy atom: .R<GLU 457>.A<CG 8>
Added missing heavy atom: .R<GLU 457>.A<CD 11>
Added missing heavy atom: .R<GLU 457>.A<OE1 12>
Added missing heavy atom: .R<GLU 457>.A<OE2 13>
Added missing heavy atom: .R<LYS 462>.A<CG 8>
Added missing heavy atom: .R<LYS 462>.A<CD 11>
Added missing heavy atom: .R<LYS 462>.A<CE 14>
Added missing heavy atom: .R<LYS 462>.A<NZ 17>
Added missing heavy atom: .R<LYS 468>.A<CE 14>
Added missing heavy atom: .R<LYS 468>.A<NZ 17>
Added missing heavy atom: .R<LYS 494>.A<CE 14>
Added missing heavy atom: .R<LYS 494>.A<NZ 17>
Added missing heavy atom: .R<LYS 512>.A<CE 14>
Added missing heavy atom: .R<LYS 512>.A<NZ 17>
Added missing heavy atom: .R<ASP 589>.A<CG 8>
Added missing heavy atom: .R<ASP 589>.A<OD1 9>
Added missing heavy atom: .R<ASP 589>.A<OD2 10>
Added missing heavy atom: .R<GLN 642>.A<CG 8>
Added missing heavy atom: .R<GLN 642>.A<CD 11>
Added missing heavy atom: .R<GLN 642>.A<OE1 12>
Added missing heavy atom: .R<GLN 642>.A<NE2 13>
Added missing heavy atom: .R<ASN 645>.A<CG 8>
Added missing heavy atom: .R<ASN 645>.A<OD1 9>
Added missing heavy atom: .R<ASN 645>.A<ND2 10>
Added missing heavy atom: .R<ASP 652>.A<CG 8>
Added missing heavy atom: .R<ASP 652>.A<OD1 9>
Added missing heavy atom: .R<ASP 652>.A<OD2 10>
Added missing heavy atom: .R<LYS 655>.A<CG 8>
Added missing heavy atom: .R<LYS 655>.A<CD 11>
Added missing heavy atom: .R<LYS 655>.A<CE 14>
Added missing heavy atom: .R<LYS 655>.A<NZ 17>
Added missing heavy atom: .R<GLN 680>.A<CG 8>
Added missing heavy atom: .R<GLN 680>.A<CD 11>
Added missing heavy atom: .R<GLN 680>.A<OE1 12>
Added missing heavy atom: .R<GLN 680>.A<NE2 13>
Added missing heavy atom: .R<LYS 692>.A<CD 11>
Added missing heavy atom: .R<LYS 692>.A<CE 14>
Added missing heavy atom: .R<LYS 692>.A<NZ 17>
Added missing heavy atom: .R<LYS 757>.A<CG 8>
Added missing heavy atom: .R<LYS 757>.A<CD 11>
Added missing heavy atom: .R<LYS 757>.A<CE 14>
Added missing heavy atom: .R<LYS 757>.A<NZ 17>
Added missing heavy atom: .R<CILE 909>.A<OXT 20>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C4D-ND-*
+--- 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: *-C1D-ND-*
+--- 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: *-CAC-CBC-*
+--- 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: *-CAB-CBB-*
+--- 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: *-C4B-NB-*
+--- 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: *-C1B-NB-*
+--- 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: *-FE-NB-*
+--- With Sp3 - 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: *-FE-ND-*
+--- With Sp3 - 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: *-C4D-ND-*
+--- 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: *-C1D-ND-*
+--- 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: *-CAC-CBC-*
+--- 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: *-CAB-CBB-*
+--- 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: *-C4B-NB-*
+--- 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: *-C1B-NB-*
+--- 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: *-FE-NB-*
+--- With Sp3 - 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: *-FE-ND-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 7333
Leap added 7433 missing atoms according to residue templates:
83 Heavy
7350 H / lone pairs
>
Thank you very much for your help!
Max
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Received on Wed Oct 31 2012 - 07:30:02 PDT
