AMBER Archive (2009)

Subject: Re: [AMBER] Non-Standard Atoms

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sat Dec 19 2009 - 20:54:20 CST

frcmod.ff99SB should be in $AMBERHOME/dat/leap/parm (or according to
your output below, /usr/local/antechamber-1.27/dat/leap/parm/ . Is
that file in there? Are there any files in there? It should be part
of ambertools 1.2 available on ambermd.org .

588 atoms not being in the template seems like quite a large number.
Do you know which atoms that is referring to? It's also adding 600+
additional hydrogens, so perhaps your hydrogens are simply not named
correctly? The names of the atoms should be in the OFF library file
in $AMBERHOME/dat/leap/lib/parm94.dat .

Good luck!
Jason

On Sat, Dec 19, 2009 at 8:56 PM, Jack Shultz <js_at_drugdiscoveryathome.com> wrote:
> First, I seem to get an error when I open tleap: frcmod.ff99SB not found.
> Where can I find this file, moreover is it needed for what I am doing?
> I'm preping a structure for analysis. It also says 588 atoms not in
> residue templates. How can I report on which atoms? Can I make leap
> ignore these atoms?
>
> tleap -s -f /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB
> -I: Adding /usr/local/antechamber-1.27/dat/leap/prep to search path.
> -I: Adding /usr/local/antechamber-1.27/dat/leap/lib to search path.
> -I: Adding /usr/local/antechamber-1.27/dat/leap/parm to search path.
> -I: Adding /usr/local/antechamber-1.27/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB.
>
> Welcome to LEaP!
> Sourcing: /usr/local/antechamber-1.27/dat/leap/cmd/leaprc.ff99SB
> Log file: ./leap.log
> Loading parameters: /usr/local/antechamber-1.27/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
> Could not open file frcmod.ff99SB: not found
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_nucleic94.lib
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_amino94.lib
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_aminoct94.lib
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/all_aminont94.lib
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/ions94.lib
> Loading library: /usr/local/antechamber-1.27/dat/leap/lib/solvents.lib
>
> ...
> Created a new atom named: HN within residue: .R<CARG 275>
>  total atoms in file: 3844
>  Leap added 608 missing atoms according to residue templates:
>       608 H / lone pairs
>  The file contained 588 atoms not in residue templates
>
>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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