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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Received on Thu Oct 15 2015 - 01:30:03 PDT
