I have tried to follow the suggestions below and ran into trouble rather
quickly, as indicated below.
Thanks again for any help,
J Woods Halley
University of Minnesota
On Thu, 31 Jul 2014, Parker de Waal wrote:
> Hi J,
>
> When leap encounters non-standard residues, that are not defined within
the loaded force field or loaded separately, you'll experience the string
of 'Unknown residue..' errors you pasted below.
>
> I would recommend reading and following the antechamber tutorial,
found here: http://ambermd.org/tutorials/basic/tutorial4b/ , to generate
topology files for the retinal and cholesterol ligands found within your pdb.
The reduce instruction on my pdb file worked all right. However the next
call to antechamber which I implemented as
antechamber -i protonpumprhodospinAR23AM6.pdb -fi pdb -o
protonpumprhodospinAR23AM6.mol2 -fo mol2 -c bcc -s 2
following the reference exactly, gave me a whole series of the following
messages followed by Segmentation Fault
Warning: detected more than 10 Residue sequence numbers;
this may be a large multiple residue PDB file;
large multiple residue PDB files are not supported.
Continuing, but problems may be encountered.
Segmentation fault
Certainly my file contains more than 10 residues. Am I supposed to
generate a separate pdb file for the RET and CLR residues? I certainly
don't know how to do that.
>
> Once you feel comfortable with ligand paramterization you could alternatively use REDs, found here: http://q4md-forcefieldtools.org/REDS/ , to derive more accurate (when using a private account uses Guassian for backend calculations) RESP charges and optimized geometry files for RET and CLR for your simulation.
>
> Just remember, when using antechamber always remember to verify the automatically assigned atom types (found in the resulting .mol2) against the GAFF atom types found here: http://ambermd.org/antechamber/gaff.html#atomtype !
>
> Best,
> Parker
> ________________________________________
> From: J.W. Halley [woods.woods1.spa.umn.edu]
> Sent: Wednesday, July 30, 2014 8:56 PM
> To: amber.ambermd.org
> Subject: [AMBER] this a very green neophyte's question.
>
> 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://scanmail.trustwave.com/?c=129&d=upLZ09QTkTK-3DJcrPm7jgUq3Wzm7fN9qJIYwvaYPw&u=http%3a%2f%2fblanco%2euci%2eedu%2fmpstruc
> 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 Thu Jul 31 2014 - 15:00:03 PDT
