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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Received on Wed Oct 14 2015 - 02:30:07 PDT
