AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: FyD (
Date: Fri Jul 10 2009 - 00:52:12 CDT

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
> 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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