Thanks again for the help but I got stock quickly trying to implement it.
I get
parm protonpumprhodospinAR23AM6.pdb
-bash: parm: command not found
same thing with trajin
Maybe I have to load something else, or maybe my system won't let me do
this?
Thanks,
Woods Halley
On Thu, 31 Jul 2014, Daniel Roe wrote:
> Hi,
>
> What you are attempting to do (parameterize ligands) is not simple,
> and easy to do wrong. If you haven't already, it may be worth it to
> look over a few of the Amber tutorials
> (http://ambermd.org/tutorials/), at least the basic ones, to
> familiarize yourself with Amber as a whole. The advanced tutorial A1
> covers developing parameters with antechamber for non-standard
> residues in MD simulations; you can also use RED server for developing
> parameters. Better yet, check in the literature (and with google) to
> see if the parameters you need have already been developed.
>
> On Thu, Jul 31, 2014 at 3:47 PM, J.W. Halley <woods.woods1.spa.umn.edu> wrote:
>> 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.
>
> You can separate these residues out using the following cpptraj input:
>
> # Load topology
> parm protonpumprhodospinAR23AM6.pdb
> # Load coordinates
> trajin protonpumprhodospinAR23AM6.pdb
> # Strip all but RET
> strip !:RET
> # Write RET out
> outtraj RET.pdb
> # Revert back to original
> unstrip
> # Strip all but CLR
> strip !:CLR
> # Write CLR out
> outtraj CLR.pdb
>
> Hope this helps,
>
> -Dan
>
>>>
>>> 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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>>> AMBER.ambermd.org
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>>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Thu Jul 31 2014 - 15:30:02 PDT
