Please find the files attached
NAP.mol2 and BG6_1.mol2 are input files which I used in antechamber and
NAP_amber.mol2 and BG6_amber.mol2 are output files of antechamber
Also when I used command
solvateBox protein TIP3PBOX 14.0 iso
it adds water however when I add ions by following command
addIonsRand complex Na+ 0
it gives me error that 'No solvent present. Add solvent first'.
Please suggest I am new to amber and facing alot of problems
thank you
On Mon, Jun 3, 2019 at 6:33 PM Gerardo Zerbetto De Palma <
g.zerbetto.gmail.com> wrote:
> PS: send the .frcmod files too.
>
> El lun., 3 jun. 2019 a las 14:31, Gerardo Zerbetto De Palma (<
> g.zerbetto.gmail.com>) escribió:
>
> > 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
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> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> >
> >> > _______________________________________________
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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
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> >>
> >
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Received on Tue Jun 04 2019 - 05:30:03 PDT
