Hello Jin
In the first method the error:
FATAL: Atom .R<BP1 481>.A<C01 29> does not have a type.
it happened to me when I made I mistake and do not specify correctly the
files for the ligand. I normally use for my ligand a *.prp and *.frcmod
files. Check that after loading the parameters for the AMBER forfield, the
gaff, ions and solvents , you load your ligand, typiclally loadoff lig.lib,
loadamberparams lig.frcmod. Because that error, most of the time is related
with not loading the files for the ligand correctly, such us reusing a
script file and forgetting to change the name of the files or the path were
they are. I know it sounds pretty basic, but sometimes the errors are.
Have a nice day,
2015-10-14 11:20 GMT+02:00 Jin Zhang <jin.zhang.umu.se>:
> Dear Amber user group
>
> I met some difficulties when generating .prmtop and .inpcrd file for the
> protein-ligand complex using coligand charges calculated with Gaussian.
>
> I have tried in two ways:
>
> Method1(failed)
> Based on the Gaussian calculation results, .lib and .frcmod file were
> produced for the coligand with antechamber. I was able to generate .prmtop
> and .inpcrd file for the ligand alone.
>
> However, when I generate these files for the complex, tleap reported as
> follows: (BP1 is the coligand name, the same name was used in .lib and
> .frcmod file by antechamber -rn BP1)
>
> Created a new atom named: H05 within residue: .R<BP1 481>
> Created a new atom named: HO07 within residue: .R<BP1 481>
> Created a new atom named: HO13 within residue: .R<BP1 481>
> Created a new atom named: H14 within residue: .R<BP1 481>
> Created a new atom named: HO16 within residue: .R<BP1 481>
> Created a new atom named: H17 within residue: .R<BP1 481>
> Created a new atom named: H18 within residue: .R<BP1 481>
> Added missing heavy atom: .R<BP1 481>.A<C13 27>
> Added missing heavy atom: .R<BP1 481>.A<C8 16>
> Added missing heavy atom: .R<BP1 481>.A<C7 14>
> Added missing heavy atom: .R<BP1 481>.A<C9 17>
> .....
> FATAL: Atom .R<BP1 481>.A<C01 29> does not have a type.
> FATAL: Atom .R<BP1 481>.A<C02 30> does not have a type.
> FATAL: Atom .R<BP1 481>.A<C03 31> does not have a type.
> FATAL: Atom .R<BP1 481>.A<O04 32> does not have a type.
> FATAL: Atom .R<BP1 481>.A<C05 33> does not have a type.
> FATAL: Atom .R<BP1 481>.A<C06 34> does not have a type.
>
> Method2 (works)
> But I can generate .prmtop and .inpcrd file for the complex, if I load
> protein and ligand files and parameters separately and combine them
> together using combine {Protein Ligand} command in tleap.
>
> Could you please tell where the potential mistake is?
>
> Is it appropriate to generate .prmtop and .inpcrd files for complex with
> the method 2?
>
> One more questions on Gaussian settings:
> I used the settings as follows:
> "#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) iop(6/50=1) opt
> nosymm"
>
> I saw someone posted that "nosymm" will keep the ligand rigid and avoid
> potential errors. Is that true? Or I can also skip "nosymm "
> (I use Gaussian09 D01)
>
> Thanks a lot for your help!
>
> Cheers
>
>
>
>
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Wed Oct 14 2015 - 04:00:03 PDT
