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
>> > >>
>> > > _______________________________________________
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>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> > _______________________________________________
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>> >
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>>
>
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Received on Mon Jun 03 2019 - 11:00:02 PDT
