Hello Sir,
I saved topology files for ligand successfully but in case of protein I am
getting the following error. I used the commands as :
>source leaprc.ff99SB
>saveAmberParm receptor rec.top rec.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: -3.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - CT
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: CT - SH - SH
Building proper torsion parameters.
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
** No torsion terms for HS-SH-SH-CT
** No torsion terms for HS-SH-SH-HS
** No torsion terms for CT-SH-SH-CT
** No torsion terms for CT-SH-SH-HS
Building improper torsion parameters.
total 1854 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
I also tried the same with leaprc.14ffSB, but also gave errors.
Thank you.
Best Regards,
*Neha*
Research Scholar,
Centre for Computational Biology and Bioinformatics,
School of Life Sciences,
Central University of Himachal Pradesh,
On Thu, Jan 7, 2016 at 6:51 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Jan 7, 2016 at 7:26 AM, neha chaudhary <nehachaudhary769.gmail.com
> >
> wrote:
>
> > Hi,
> >
> > For ligand, i first used antechamber as
> > >antechamber -i ligand.mol2 -fi mol2 -o ligand.prep -fo prepi
> > >parmchk -i ligand.prep -f prepi -o ligand.frcmod
> > >tleap
> > >source leaprc.gaff
> > >loadAmberParams ligand.frcmod
> > >LIG = loadMol2 ligand.mol2
> >
>
> This looks wrong. Your antechamber command used ligand.mol2 as an *input*
> and generated ligand.prep as an output. The antechamber output --
> ligand.prep -- is the file that contains the atom types and charges for
> your ligand (as assigned by antechamber). Generally when people use
> antechamber, they have a PDB file of their ligand and they use that to make
> a mol2 file with atom types and charges. You should double-check where you
> got your ligand.mol2 file and make sure you are not doing the antechamber
> step twice, for instance.
>
> Regardless of what you do, it is the *output* of the antechamber step that
> you should be loading into tleap, not the input. So this should be
> something like "loadAmberPrep ligand.prep" instead of loading the mol2
> file. Also, I believe that the residue name for your ligand is set inside
> the prep file, so make sure that it is called "LIG" inside the prep file if
> the ligand has that residue name in your complex/protein PDB file.
>
> >saveAmberParm LIG ligand.top ligand.crd
> >
> > ligand topology files generated without error.
> >
> > For protein:
> >
> > >tleap
> > >source leaprc.gaff
> > >receptor = loadPDB protein.pdb
> >
>
> In addition to what Dave said, you *also* need to load the ligand residue
> template and parameter files. So you need something like
>
> loadAmberParams ligand.frcmod
> loadAmberPrep ligand.prep
>
> I highly recommend going over some of the antechamber tutorials at
> http://ambermd.org/tutorials. They will probably help clear up many
> misunderstandings.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Jan 12 2016 - 04:00:03 PST
