Dear Aron,
Thank you for your prompt response. It turns out that it was a formatting problem. The NEWPDB.PDB file was missing the residue name (arbitrarily set to MOL in the prep file for consistency) beginning at column number 18. Caution must be exerted in employing different software programs to generate pdb files due to "subtle" differences in pdb formatting. For instance, the pdb files created by GaussView and VEGAZZ incur slight differences as well as differences in the pdb files generated by Antechamber. Your suggestion was correct and helpful: ultimately, tleap was having trouble associating the prep file with the pdb file. Thank you for your help.
Regards,
Marco
> Date: Wed, 8 Feb 2012 01:33:16 -0500
> From: broomsday.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] error in tleap execution of loadpdb
>
> Hi Marco,
>
> Do you have a *.lib file for the fragment? I imagine the prep file is very
> similar but I've never used them.
>
> One potential problem might be the leap is not recognizing from your PDB
> that the molecule you have there is supposed to match with your prep file.
> In your prep file the molecule is named "INT.0" (molecule.residue), whereas
> in your PDB you simply have it being residue 0, but have not named it INT.
> I maybe wrong, but I think it is like have a PDB with as aspartic acid, but
> deleting the ASP keyword for each atom entry, it will no longer work.
>
> Anyway, that's my only quick suggestion.
>
> ~Aron
>
> On Wed, Feb 8, 2012 at 1:09 AM, <molguin.miners.utep.edu> wrote:
>
> >
> > Hello,
> >
> > I have encountered a problem in the
> > loadpdb execution of tleap. I am trying to generate prmtop and prmcrd
> > files for a molecular triad composed of Carotenoid-Porphyrin-C60
> > subunits. Before attempting antechamber/tleap runs for the triad, I am
> > working on each of the three subunits separately. Consequently, I have
> > successfully generated prep and frcmod files for each component with the
> > use of antechamber. Next, the following script (leap.in) was run with
> > tleap (./tleap -s -f leap.in) for a C60-pyrolle molecule.
> >
> > %%%
> > antechamber command used: ./antechamber -i Frag_C60-pyrolle.pdb -fi
> > pdb -o Frag_C60-pyrolle.prep -fo prepi -c gas -j 4 -at gaff -du y
> > %%% parmchk command used: ./parmchk -i Frag_C60-pyrolle.prep -f prepi -o
> > Frag_C60-pyrolle.frcmod -p gaff.dat -w Y
> >
> > leap.in:
> > LoadAmberParams gaff.dat
> > LoadAmberParams Frag_C60-pyrolle.frcmod
> > LoadAmberPrep Frag_C60-pyrolle.prep
> > sys = loadpdb NEWPDB.PDB
> > saveAmberParm sys C.top C.crd
> > quit
> >
> > I
> > looked extensively through the amber archives and encountered several
> > discussions closely related to the error message that I receive and will
> > display below. From what I understand, the pdb file loaded by tleap
> > through the loadpdb command does not make use of the atom types
> > corresponding to the gaff force field atom types (such as those
> > displayed in the prep file). In fact, tleap states that the atom names
> > should be unique for each residue. In my case, the entire C60-pyrolle
> > molecule is one residue. I have attached 2 different input pdb files
> > that I ran in tleap (NEWPDB.PDB and Test.pdb), the prep file, and the
> > frcmod file. In addition, I have attached a log file (tleap.log)
> > containing the entire error message given by the tleap program since
> > below is included only an excerpt. Thank you very much for your time.
> > Any suggestions would be greatly appreciated.
> >
> > Regards,
> > Marco Olguin
> > Graduate Student
> > University of Texas at El Paso
> >
> > Error Message:
> > Welcome to LEaP!
> > Sourcing: ./leap.in
> > Loading parameters: ./gaff.dat
> > Reading title:
> > AMBER General Force Field for organic molecules (Version 1.4, March 2010)
> > add. info. at the end
> > Loading parameters: ./Frag_C60-pyrolle.frcmod
> > Reading force field modification type file (frcmod)
> > Reading title:
> > remark goes here
> > Loading Prep file: ./Frag_C60-pyrolle.prep
> > Loading PDB file: ./NEWPDB.PDB
> > Unknown residue: number: 0 type: Terminal/last
> > ..relaxing end constraints to try for a dbase match
> > -no luck
> > Creating new UNIT for residue: sequence: 0
> > Created a new atom named: C25 within residue: .R< 0>
> > Created a new atom named: C7 within residue: .R< 0>
> > Created a new atom named: C22 within residue: .R< 0>
> > Created a new atom named: C5 within residue: .R< 0>
> > Created a new atom named: C23 within residue: .R< 0>
> > Created a new atom named: C36 within residue: .R< 0>
> > Created a new atom named: C15 within residue: .R< 0>
> > ..................
> > FATAL: Atom .R< 0>.A<H3 70> does not have a type.
> > FATAL: Atom .R< 0>.A<C63 71> does not have a type.
> > FATAL: Atom .R< 0>.A<H6 72> does not have a type.
> > FATAL: Atom .R< 0>.A<C66 73> does not have a type.
> > FATAL: Atom .R< 0>.A<H2 74> does not have a type.
> > FATAL: Atom .R< 0>.A<C65 75> does not have a type.
> > FATAL: Atom .R< 0>.A<H1 76> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> > Quit
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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Received on Wed Feb 08 2012 - 21:30:02 PST
