Dear Maria,
Thank you for the reply.
Actually i did load my mol2 file before the frcmod and .lib files before
the pdb complex file. But it was not recognised also.
I used the command
Tleap - f leaprc.protein.ff14SB
Source leaprc.gaff
lig = loadmol2 lig.mol2
loadamberparams lig.frcmod
Loadoff lig.lib
Complex =loadpdb complex.pdb
Is it the correct command?
Thank you again
Regards
Ayesha
On Fri, 28 Aug 2020, 7:02 am Maria Nagan, <maria.c.nagan.gmail.com> wrote:
> For some reason I didn’t see your original post with the files.
>
> Did you load your ccl2_fragH.mol2 file into leap before you added your pdb
> file?
> Did you rename your ccl2_fragH.mol2 residue name PCA in your mol2 file?
>
> You’re right your new non-standard residue is not being recognized. Every
> non-standard residue needs to have a .lib file (or mol2 file) and an frcmod
> file loaded. If you look at some of the leaprc files available, you will
> see that they always load in an lib file and then the frcmod file. You have
> to tell leap the you have a new residue named PCA with certain atom types.
> Then you need to load in an frcmod file that tells leap that your new PCA
> residue has parameters.
>
> --Maria
>
> > On Aug 27, 2020, at 6:42 PM, Ayesha Fatima <ayeshafatima.69.gmail.com>
> wrote:
> >
> > Good morning everyone.
> > I am having the same problem. I posted my question but it is waiting
> > approval to be posted as i wrote it too long, pethaps.
> > Thank you
> > Regards
> >
> > On Fri, 28 Aug 2020, 3:56 am Erika Davidoff, <erikadavidoff.gmail.com>
> > wrote:
> >
> >> Dear Amber users,
> >>
> >> I am new to computational modeling and have an issue I've been trying to
> >> solve. I am working with a PDB of a protein that has mostly standard
> >> residues and one non-standard HETATM called PCA that contains 8 atoms.
> To
> >> get the parameters for this non-standard residue, I made a separate PDB
> >> with the one residue, added hydrogens to it and used antechamber to
> >> generate a mol2 file:
> >>
> >> antechamber -i ccl2_fragH.pdb -fi pdb -o ccl2_fragH.mol2 -fo mol2 -at
> amber
> >> -c bcc
> >>
> >>
> >> Then I used parmchk2 to generate a modified force field parameters file
> >> that has a lot of parameters:
> >>
> >> parmchk2 -i ccl2_fragH.mol2 -f mol2 -o ccl2.frcmod
> >>
> >>
> >> Then I have a tleap script that includes the lines
> >>
> >> loadamberparams ccl2.frcmod
> >>
> >> ccl2 = loadPdb ccl2.pdb
> >>
> >>
> >> and proceeds to add a peptide to the system and solvate it. When I run
> >> this, I get errors for all eight atoms in the non-standard residue:
> >>
> >> Unknown residue: PCA number: 0 type: Terminal/beginning
> >>
> >> ..relaxing end constraints to try for a dbase match
> >>
> >> -no luck
> >>
> >> Creating new UNIT for residue: PCA sequence: 1
> >>
> >> Created a new atom named: N within residue: .R<PCA 1>
> >>
> >> Created a new atom named: CA within residue: .R<PCA 1>
> >>
> >> Created a new atom named: CB within residue: .R<PCA 1>
> >>
> >> Created a new atom named: CG within residue: .R<PCA 1>
> >>
> >> Created a new atom named: CD within residue: .R<PCA 1>
> >>
> >> Created a new atom named: OE within residue: .R<PCA 1>
> >>
> >> Created a new atom named: C within residue: .R<PCA 1>
> >>
> >> Created a new atom named: O within residue: .R<PCA 1>
> >>
> >> ...
> >>
> >> FATAL: Atom .R<PCA 9>.A<O 8> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<C 7> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<OE 6> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<CD 5> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<CG 4> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<CB 3> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<CA 2> does not have a type.
> >>
> >> FATAL: Atom .R<PCA 9>.A<N 1> does not have a type.
> >>
> >>
> >> I have attached: ccl2.pdb, the original protein file (straight from the
> >> database); ccl2_fragH.pdb, the file with the one residue; ccl2.frcmod;
> and
> >> my tleap script.
> >>
> >> Thank you for your help!
> >>
> >> Best,
> >> Erika
> >>
> >> *Erika J. Davidoff *
> >> *Rutgers University*
> >> Department of Biomedical Engineering
> >> _______________________________________________
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> >>
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>
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Received on Thu Aug 27 2020 - 18:00:02 PDT
