Hi MarcZhang.
Can you copy the instructions that you give tLeap for generating the
topology and coordinates file of the complex?
Thanks
2015-10-15 10:23 GMT+02:00 MarcZhang <progress0935zhang.gmail.com>:
> 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.
>
>
>
> 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.
>
>
>
> I did check that BP1 ligand parameter was correctly loaded:
>
> > list
>
> ACE ALA ARG ASH ASN ASP BP1
>
> CALA CARG CASN CASP CCYS CCYX CGLN CGLU
>
>
> CGLY CHCL3BOX CHID CHIE CHIP CHIS CILE CIO
>
>
> CLEU CLYS CMET CPHE CPRO CSER CTHR CTRP
>
>
> CTYR CVAL CYM CYS CYX Cl- Complex Cs+
>
>
> DA DA3 DA5 DAN DC DC3 DC4 DC5
>
>
> DCN DG DG3 DG5 DGN DT DT3 DT5
>
>
> DTN GLH GLN GLU GLY HID HIE HIP
>
>
> HIS HOH IB ILE K+ LEU LYN LYS
>
>
> Li+ MEOHBOX MET MG2 NALA NARG NASN NASP
>
>
> NCYS NCYX NGLN NGLU NGLY NHE NHID NHIE
>
>
> NHIP NHIS NILE NLEU NLYS NMABOX NME NMET
>
>
> NPHE NPRO NSER NTHR NTRP NTYR NVAL Na+
>
>
> PHE PL3 POL3BOX PRO QSPCFWBOX RA RA3 RA5
>
>
> RAN RC RC3 RC5 RCN RG RG3 RG5
>
>
> RGN RU RU3 RU5 RUN Rb+ SER SPC
>
>
> SPCBOX SPCFWBOX SPF SPG T4E THR TIP3PBOX
> TIP3PFBOX
>
> TIP4PBOX TIP4PEWBOXTIP5PBOX TP3 TP4 TP5 TPF TRP
>
>
> TYR VAL WAT frcmod99SBgaff parm99
>
>
>
> > check BP1
>
> Checking 'BP1'....
>
> Checking parameters for unit 'BP1'.
>
> Checking for bond parameters.
>
> Checking for angle parameters.
>
> Unit is OK.
>
>
>
> Can someone tell where the potential error is?
>
>
>
> Thanks a lot in advances.
>
>
>
> Cheers
>
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>
--
Dr. Emilio Lence Quintana
Organic Chemistry Department-CIQUS
University of Santiago de Compostela
15782 Santiago de Compostela, Spain
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Received on Thu Oct 15 2015 - 02:30:02 PDT
