Hi J,
Antechamber cannot be run on the whole protein+ligand complex.
I would recommend using PyMOL, if you don't have access to the paid version the free version will work fine, to extract a single RET and CLR ligand from the 3AM6.pdb and save them as RET.pdb and CLR.pdb respectively.
Once this is done you can use antechamber to parameterize the ligands individually.
Best,
Parker
________________________________________
From: J.W. Halley [woods.woods1.spa.umn.edu]
Sent: Thursday, July 31, 2014 5:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] this a very green neophyte's question.
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://scanmail.trustwave.com/?c=129&d=z7fa05I9EtgNzEL78MwGV95IsGZ5w25tZqIp8vDQrw&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2fbasic%2ftutorial4b%2f , 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://scanmail.trustwave.com/?c=129&d=z7fa05I9EtgNzEL78MwGV95IsGZ5w25tZqIp86HRrA&u=http%3a%2f%2fq4md-forcefieldtools%2eorg%2fREDS%2f , 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://scanmail.trustwave.com/?c=129&d=z7fa05I9EtgNzEL78MwGV95IsGZ5w25tZvVx8_DbrQ&u=http%3a%2f%2fambermd%2eorg%2fantechamber%2fgaff%2ehtml%23atomtype !
>
> 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=z7fa05I9EtgNzEL78MwGV95IsGZ5w25tZvQm9fWL-g&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 - 15:00:04 PDT
