I am trying to get started using Amber. At Minnesota, Amber (11 I think)
is available on the Minnesota Supercomputing Center machine Itasca
and I have downloaded a .pdb file of a membrane protein of interest to
me from the site /
http://blanco.uci.edu/mpstruc
The file displays nicely with rasmol. I read the Ambertools manual and
followed the procedure on p. 49 of the posted Ambertools with the
following results (after loading the Amber module)
tleap
>source leaprc.ff99SB
Loading library: /soft/amber/11/dat/leap/lib/all_nucleic94.lib
Loading library: /soft/amber/11/dat/leap/lib/all_amino94.lib
Loading library: /soft/amber/11/dat/leap/lib/all_aminoct94.lib
Loading library: /soft/amber/11/dat/leap/lib/all_aminont94.lib
Loading library: /soft/amber/11/dat/leap/lib/ions94.lib
Loading library: /soft/amber/11/dat/leap/lib/solvents.lib
Substituting map 0ALA -> NALA for 0ALA -> NALA
(long list of substitutions follows)
>test5 = loadPdb protonpumprhodospinAR23AM6.pdb
Loading PDB file: ./protonpumprhodospinAR23AM6.pdb
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain D)
Unknown residue: RET number: 896 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: CLR number: 897 type: Nonterminal
Unknown residue: CLR number: 898 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: RET number: 899 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: CLR number: 900 type: Nonterminal
Unknown residue: CLR number: 901 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: RET number: 902 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: CLR number: 903 type: Nonterminal
Unknown residue: CLR number: 904 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: RET number: 905 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: CLR number: 906 type: Nonterminal
Unknown residue: CLR number: 907 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<CLYS 224>.A<OXT 23>
Added missing heavy atom: .R<CLYS 448>.A<OXT 23>
Added missing heavy atom: .R<CLYS 672>.A<OXT 23>
Added missing heavy atom: .R<CLYS 896>.A<OXT 23>
Creating new UNIT for residue: RET sequence: 897
Created a new atom named: C1 within residue: .R<RET 897>
Created a new atom named: C2 within residue: .R<RET 897>
(long list of 'new atoms' follows ending with
Created a new atom named: C27 within residue: .R<CLR 908>
Created a new atom named: O1 within residue: .R<CLR 908>
total atoms in file: 7328
Leap added 7084 missing atoms according to residue templates:
4 Heavy
7080 H / lone pairs
The file contained 304 atoms not in residue templates
> saveAmberParm test5 prmtop prmcrd
Checking Unit.
WARNING: There is a bond of 3.366723 angstroms between:
------- .R<PRO 35>.A<C 13> and .R<LEU 36>.A<N 1>
WARNING: There is a bond of 4.779719 angstroms between:
------- .R<ASP 154>.A<C 11> and .R<LYS 155>.A<N 1>
WARNING: There is a bond of 3.374418 angstroms between:
------- .R<PRO 259>.A<C 13> and .R<LEU 260>.A<N 1>
WARNING: There is a bond of 4.775943 angstroms between:
------- .R<ASP 378>.A<C 11> and .R<LYS 379>.A<N 1>
WARNING: There is a bond of 3.365572 angstroms between:
------- .R<PRO 483>.A<C 13> and .R<LEU 484>.A<N 1>
WARNING: There is a bond of 4.771040 angstroms between:
------- .R<ASP 602>.A<C 11> and .R<LYS 603>.A<N 1>
WARNING: There is a bond of 3.339710 angstroms between:
------- .R<PRO 707>.A<C 13> and .R<LEU 708>.A<N 1>
WARNING: There is a bond of 4.770351 angstroms between:
------- .R<ASP 826>.A<C 11> and .R<LYS 827>.A<N 1>
WARNING: The unperturbed charge of the unit: -24.000000 is not zero.
FATAL: Atom .R<RET 897>.A<C1 1> does not have a type.
FATAL: Atom .R<RET 897>.A<C2 2> does not have a type.
FATAL: Atom .R<RET 897>.A<C3 3> does not have a type.
(long list of fatal errors follows ending with)
FATAL: Atom .R<CLR 908>.A<C26 26> does not have a type.
FATAL: Atom .R<CLR 908>.A<C27 27> does not have a type.
FATAL: Atom .R<CLR 908>.A<O1 28> does not have a type.
Failed to generate parameters
Parameter file was not saved.
I repeated this frustrating procedure with at least one other pdb file
from the same site.
The manual says something about using "addPdbAtomMap or
addPdbResMap commands to make systematic changes from the names in your
PDB files" in cases like this but looking at the description of those
commands, I have to know what names to use, and I do not.
Would using another 'leaprc...' file as source be likely to help?
I'm sorry for the length of this post and will be grateful for any help.
Thank you,
J Woods Halley
Physics Department
University of Minnesota
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Received on Wed Jul 30 2014 - 18:00:02 PDT
