Re: [AMBER] Antechamber ligand parametrization

From: Parker de Waal <Parker.deWaal.vai.org>
Date: Thu, 18 Sep 2014 11:21:04 +0000

James,

I would highly recommend reading through and completing the amber tutorial
for ligand paramaterization.
http://ambermd.org/tutorials/basic/tutorial4b/


Looking at your leap input the following command jumps out at me: 'protein
= loadmol2 ligand.mol2╣. In order for this to correspond with the frcmod
and lib files, hopefully both named MOL you would need to run îMOL =
loadmol2 ligand.mol2╣ and then run check MOL.

I have a hunch this will fix your errors.

Parker

On 9/17/14, 9:02 AM, "James Starlight" <jmsstarlight.gmail.com> wrote:

>Yes sure I've tried to applied parametrization of the ligand.pdb file
>(stripped from hydrogens) produced by autodock with the tleap and its
>produced errors that each atom type of the ligand has not been found:
>
>Unknown residue: MOL number: 0 type: Terminal/last
>..relaxing end constraints to try for a dbase match
> -no luck
>Creating new UNIT for residue: MOL sequence: 1
>Created a new atom named: C1 within residue: .R<MOL 1>
>Created a new atom named: C2 within residue: .R<MOL 1>
>Created a new atom named: C3 within residue: .R<MOL 1>
>Created a new atom named: C4 within residue: .R<MOL 1>
>Created a new atom named: C5 within residue: .R<MOL 1>
>Created a new atom named: C6 within residue: .R<MOL 1>
>Created a new atom named: H7 within residue: .R<MOL 1>
>Created a new atom named: H8 within residue: .R<MOL 1>
>Created a new atom named: H9 within residue: .R<MOL 1>
>Created a new atom named: H10 within residue: .R<MOL 1>
>Created a new atom named: H11 within residue: .R<MOL 1>
>Created a new atom named: C12 within residue: .R<MOL 1>
>Created a new atom named: H13 within residue: .R<MOL 1>
>Created a new atom named: H14 within residue: .R<MOL 1>
>Created a new atom named: O15 within residue: .R<MOL 1>
>Created a new atom named: C16 within residue: .R<MOL 1>
>Created a new atom named: O17 within residue: .R<MOL 1>
>Created a new atom named: C18 within residue: .R<MOL 1>
>Created a new atom named: H19 within residue: .R<MOL 1>
>Created a new atom named: H20 within residue: .R<MOL 1>
>Created a new atom named: H21 within residue: .R<MOL 1>
> total atoms in file: 21
> The file contained 21 atoms not in residue templates
>Checking 'protein'....
>FATAL: Atom .R<MOL 1>.A<C1 1> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C2 2> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C3 3> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C4 4> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C5 5> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C6 6> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H7 7> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H8 8> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H9 9> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H10 10> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H11 11> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C12 12> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H13 13> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H14 14> does not have a type.
>FATAL: Atom .R<MOL 1>.A<O15 15> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C16 16> does not have a type.
>FATAL: Atom .R<MOL 1>.A<O17 17> does not have a type.
>FATAL: Atom .R<MOL 1>.A<C18 18> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H19 19> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H20 20> does not have a type.
>FATAL: Atom .R<MOL 1>.A<H21 21> does not have a type.
>
>
>here I've provided to tleap all files generated on the previous step by
>anthechamber ( I have no such problem with the parametrization of the mol2
>file produced by anthechamber too where I have the same naming for all the
>atoms with the expeption of hydrogens):
>
># for tleap
>source leaprc.ff03.r1
>source leaprc.gaff
>loadamberparams /ligand/ligand.frcmod
>loadoff /ligand/ligand.lib
>#protein = loadpdb test.pdb
>protein = loadmol2 ligand.mol2
>check protein
>savepdb protein test.pdb
>quit
>
>James
>
>2014-09-17 13:40 GMT+02:00 David A Case <case.biomaps.rutgers.edu>:
>
>> On Wed, Sep 17, 2014, James Starlight wrote:
>>
>> > because (superimposed to the receptor cavity)
>> > ligand.pdb produced by autodock have been stripped from all
>>hydrogen╣s so
>> > its coordinates not equal to initial ligand.mol2 . Will it possible
>>using
>> > amber's ligand.lib to restore full-atomic structure of the ligand
>>based
>> on
>> > its (no H) coordinates obtained from docking?
>>
>> What went wrong when you tried this?
>>
>> Generally, if you are wondering how to do something in Amber, the best
>> approach is to run some experiments to see what happens.
>>
>> ...dac
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>>http://scanmail.trustwave.com/?c=129&d=goaZ1OjvD-_6wJGHJo-YPRLH1-Bx0tojoI
>>4VryzSig&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2fambe
>>r
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://scanmail.trustwave.com/?c=129&d=goaZ1OjvD-_6wJGHJo-YPRLH1-Bx0tojoI4
>VryzSig&u=http%3a%2f%2flists%2eambermd%2eorg%2fmailman%2flistinfo%2famber


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 18 2014 - 04:30:04 PDT
Custom Search