Dear Sadaf Rani,
You are solvating the unit "protein" but are requesting to add ions to unit "complex"...
If your PDB file contains both protein and ligands, then there is no need for such "complex" unit... notice that .mol2 files may have different XYZ coordinates than those in the PDB structure...
I also noticed that the residue name in "NAP_amber.mol2" is "LIG" instead of "NAP", that's not an issue for generating the topology however the residue will be renamed from NAP (in the PDB structure) to LIP in the AMBER topology and any PDB file generated afterwards...
In case of BG6_amber.mol2 there is an atom belonging to residue 2UNK" that's odd... I suppose they all should be within residue "BG6".
Best,
Matías
----- Mensaje original -----
De: "Sadaf Rani" <sadafrani6.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 4 de Junio 2019 9:15:01
Asunto: Re: [AMBER] tleap ERROR
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
> >> > > 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 Tue Jun 04 2019 - 09:30:02 PDT
