AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber prep question

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jul 10 2009 - 10:24:08 CDT

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 <fyd_at_q4md-forcefieldtools.org> wrote:
>
> From: FyD <fyd_at_q4md-forcefieldtools.org>
> Subject: Re: [AMBER] Antechamber prep question
> To: amber_at_ambermd.org
> 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 http://archive.ambermd.org/200812/0329.html, 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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