AMBER Archive (2009)

Subject: [AMBER] ligand/protein minimization

From: Andrew Olson (
Date: Fri Jul 10 2009 - 16:00:26 CDT

When trying to minimize my protein with ligand bound (directly from antechamber) it keeps throwing up errors in xleap (after check) that something is wrong with my ligand atom types, but i cant seem to figure it out.  Here is the error i get after i check the file using xleap.FATAL:  Atom .R<SUB 189>.A<O17 1> does not have a type.I also have a clash with ligand and a residue in the protein, will that be a problem for minimizing?  I will include the pdb file of the ligand bound to the protein for reference.  I want to keep the ligand there, even with the clash, in hopes that the minimzing will move the domain out of the way.


--- On Fri, 7/10/09, FyD <> wrote:

From: FyD <>
Subject: Re: [AMBER] Antechamber prep question
To: "AMBER Mailing List" <>
Date: Friday, July 10, 2009, 10:24 AM

Hi Andrew,

> I actually got it worked out, for some reason the connections were  all "whacky".  So i fixed them using DS visualizer (remaded bonds,  added double bonds where there should be), saved as mol2 file and  antechamber works fine now.  
> I actually have another question, do i merge this new mol2 file and  my protein and do MD on that, sorry for the naive question there is  noone to ask in my lab.  Or do i haev to set up some how different  amber input files for each file and merge those?  Thanks

You need to prepare a FF library for ATP with correct atom names/FF atom types & charges (i. e. your mol2 file): You load the amber FF you wish to use + this ATP FF library in LEaP.

Then, when you are going to load your initial structure containing your complex (usually in the PDB format), the residue names & atom names available in this complex/PDB file have to match these available in the FF libraries. If so, you will be able to generate the prmtop/prmcrd files.

regards, Francois

> --- On Fri, 7/10/09, FyD <> wrote:
> From: FyD <>
> Subject: Re: [AMBER] Antechamber prep question
> To:
> Date: Friday, July 10, 2009, 12:52 AM
> Dear Andrew,
>> I have perused the archives and found similar topics but i still   cant figure this out.  I have a ligand that was docked using   Autodock and im now attempting to insert into the receptor to run   some MD on it.  So im trying to correct the atom types and charges   using antechamber.  I am following the basic tutorial on  antechamber  so im attempting to convert my pdb to mol2 but i get  this error that  alot of people are getting;
>> [pcp]:Research/AMBER/ATP] NAME% $AMBERHOME/bin/antechamber -i   atp_H_1.pdb -fi pdb -o ATP.mol2 -fo mol2 -c bcc
>> For atom[7]:O5, the best APS is not zero, bonds involved by this   atom are frozen
>> The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8   (aromatic double)Error: cannot run   "/usr/local/Amber10/amber10/bin/bondtype -j full -i   ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in   judgebondtype() of antechamber.c properly, exit
>> I add H's everywhere and charges (Not sure if that is necessary)   using chimera and run the same command and i get;
>> 4 is not a valid atom id in CONECT    4   22    5    2   40
> If you look at, we can  provide you many cofactors for different FF versions (& not only  ATP). The charges and FF libraries were built using a global  procedure//building block approach in a single R.E.D. job, and not  each factor taken individually.
> For instance it was possible to build AMP, ADP, ATP, AQP and more  generally XYP, X = (d)A, (d)C, G, (d)T & (d)Y, = M, D, T, etc... and  even more.
> regards, Francois

AMBER mailing list

AMBER mailing list