Created a new atom named: CL1 within residue: .R<ZCL 192>
Created a new atom named: BR1 within residue: .R<ZCL 192>
Added missing heavy atom: .R<ZCL 192>.A<****Br1***** 32>
Added missing heavy atom: .R<ZCL 192>.A<****Cl1***** 28>
HETATM 28 CL1 ZCL 900 29.703 -2.294 43.926 1.00
0.00 Cl
HETATM 32 BR1 ZCL 900 31.570 2.781 43.700 1.00
0.00 Br
The atom names are full-caps in pdb, mixed-case in your molecule definition.
Bill
On 9/11/16 8:37 PM, 康宁 wrote:
> Dear Amber users:
>
> I'm trying to create ligand leap input files for MD, and I got two problems.
>
> 1.When I used "reduce" to add hydrogen to ligand, "reduce" didn't work.
> Here was the output showed on terminal:
>
> Database of HETATM connections: "/export/apps/amber14/dat/reduce_wwPDB_het_dict.txt"
> VDW dot density = 16/A^2
> Orientation penalty scale = 1 (100%)
> Eliminate contacts within 3 bonds.
> Ignore atoms with |occupancy| <= 0.01 during adjustments.
> Waters ignored if B-Factor >= 40 or |occupancy| < 0.66
> Aromatic rings in amino acids accept hydrogen bonds.
> Building or keeping OH & SH Hydrogens.
> Rotating NH3 Hydrogens.
> Processing Met methyls.
> Found 0 hydrogens (0 hets)
> Standardized 0 hydrogens (0 hets)
> Added 0 hydrogens (0 hets)
> Removed 0 hydrogens (0 hets)
>
> The ligand file please see attachment.
>
> 2.To solve above problem, I used other software to add hydrogen, and created the lib file and frcmod file.
> And then I loaded these parameter files in tleap, everything was OK.
> But when I loaded protein-ligand complex in tleap, terminal showed as following:
>
>> cdc-zcl = loadpdb Cdc42-GDP-ZCL278-MG.pdb
> Loading PDB file: ./Cdc42-GDP-ZCL278-MG.pdb
> (starting new molecule for chain )
> Added missing heavy atom: .R<CVAL 189>.A<OXT 17>
> Created a new atom named: CL1 within residue: .R<ZCL 192>
> Created a new atom named: BR1 within residue: .R<ZCL 192>
> Added missing heavy atom: .R<ZCL 192>.A<Br1 32>
> Added missing heavy atom: .R<ZCL 192>.A<Cl1 28>
> total atoms in file: 1540
> Leap added 1535 missing atoms according to residue templates:
> 3 Heavy
> 1532 H / lone pairs
> The file contained 2 atoms not in residue templates
>
> Cl and Br are common in molecule, so why can't tleap identify these two molecule?
>
> Thanks for the help!
>
> Regards
>
>
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Received on Sun Sep 11 2016 - 21:30:03 PDT
