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
--
Kang Ning
School of Pharmacy
Shanghai Jiao Tong University
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- application/x-palm-database attachment: zcl278.pdb
Received on Sun Sep 11 2016 - 21:00:02 PDT
