AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: Andrew Olson (
Date: Fri Jul 10 2009 - 08:33:09 CDT

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

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

From: FyD <>
Subject: Re: [AMBER] Antechamber prep question
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

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