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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>>
>
>
>
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--
-------------------------
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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Received on Thu Jul 31 2014 - 15:30:02 PDT
