It seems that atoms are not defined for residues names you are using in
your input files. Send the .pdb and .mol2 files to check.
Regards
Gera!
El lun., 3 jun. 2019 a las 14:20, Sadaf Rani (<sadafrani6.gmail.com>)
escribió:
> thank you David and Gerardo
> It worked
> but my parameters are not being saved.
> It gives following
> > saveamberparm complex complex.prmtop complex.inpcrd
> Checking Unit.
> FATAL: Atom .R<BG6 517>.A<O6 16> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C6 15> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O5 14> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C5 13> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O4 12> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C4 11> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O3 10> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C3 9> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O2 8> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C2 7> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O1 6> does not have a type.
> FATAL: Atom .R<BG6 517>.A<C1 5> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O3P 4> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O2P 3> does not have a type.
> FATAL: Atom .R<BG6 517>.A<O1P 2> does not have a type.
> FATAL: Atom .R<BG6 517>.A<P 1> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N9A 48> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C8A 47> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O7N 46> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N7N 45> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N7A 44> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C7N 43> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N6A 42> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C6N 41> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C6A 40> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O5D 39> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O5B 38> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C5N 37> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C5D 36> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C5B 35> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C5A 34> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O4D 33> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O4B 32> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C4N 31> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C4D 30> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C4B 29> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C4A 28> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O3X 27> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O3D 26> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O3B 25> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O3 24> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N3A 23> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C3N 22> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C3D 21> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C3B 20> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O2X 19> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O2N 18> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O2D 17> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O2B 16> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O2A 15> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C2N 14> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C2D 13> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C2B 12> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C2A 11> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O1X 10> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O1N 9> does not have a type.
> FATAL: Atom .R<NAP 516>.A<O1A 8> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N1N 7> does not have a type.
> FATAL: Atom .R<NAP 516>.A<N1A 6> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C1D 5> does not have a type.
> FATAL: Atom .R<NAP 516>.A<C1B 4> does not have a type.
> FATAL: Atom .R<NAP 516>.A<PN 3> does not have a type.
> FATAL: Atom .R<NAP 516>.A<PA 2> does not have a type.
> FATAL: Atom .R<NAP 516>.A<P2B 1> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
> > quit
> what to do for that
>
> regards
> Sadaf
>
> On Mon, Jun 3, 2019 at 5:19 PM Aidan Reynolds <aidanreynolds1122.gmail.com
> >
> wrote:
>
> >
> > > On Jun 3, 2019, at 11:54 AM, Gerardo Zerbetto De Palma <
> > g.zerbetto.gmail.com> wrote:
> > >
> > > Hi! You should load a pdb in the unit "protein" using: protein =
> loadpdb
> > > peptide.pdb
> > > Regards!
> > > Gera!
> > >
> > > El lun., 3 jun. 2019 a las 11:25, Sadaf Rani (<sadafrani6.gmail.com>)
> > > escribió:
> > >
> > >> Dear AMBER users
> > >> I am trying to build a protein ligand system in tleap
> > >> I am doing following:-
> > >> source leaprc.protein.ff14SB
> > >> source leaprc.gaff2
> > >> source leaprc.water.tip3p
> > >>
> > >> ligA = loadmol2 NAP_amber.mol2
> > >> ligA = loadmol2 BG6_amber.mol2
> > >>
> > >> loadamberparams NAP_amber.frcmod
> > >> loadamberparams BG6_amber.frcmod
> > >>
> > >>
> > >> protein = peptide.pdb
> > >> complex = combine {protein ligA ligB}
> > >>
> > >> it gives me following error:
> > >> combine: protein is type String
> > >> expected UNIT
> > >>
> > >> I did list in tleap and it shows protein
> > >> how to correct it where I am wrong
> > >> please tell me
> > >> Thank you
> > >>
> > >> Sadaf
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Mon Jun 03 2019 - 11:00:02 PDT
