hello Ben:
I found that the script for CHARMM-GUI have some problem for the
protein atom name, I first delete all the protein hydrogen atoms and load with
tleap by command:
tleap -s -f leaprc.ff12SB
set default FlexibleWater on
source leaprc.lipid11
mol = loadpdb charmmgui.pdb
it goes well for lipids, but for protein, here is the log
--------------log-----------------------------------------------------------------
residue sequence numbers will not correspond to those in the pdb.
Created a new atom named: CD within residue: .R<ILE 24>
Added missing heavy atom: .R<ILE 24>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 25>
Added missing heavy atom: .R<ILE 25>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 37>
Added missing heavy atom: .R<ILE 37>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 45>
Added missing heavy atom: .R<ILE 45>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 53>
Added missing heavy atom: .R<ILE 53>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 55>
Added missing heavy atom: .R<ILE 55>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 59>
Added missing heavy atom: .R<ILE 59>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 60>
Added missing heavy atom: .R<ILE 60>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 64>
Added missing heavy atom: .R<ILE 64>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 70>
Added missing heavy atom: .R<ILE 70>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 84>
Added missing heavy atom: .R<ILE 84>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 138>
Added missing heavy atom: .R<ILE 138>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 140>
Added missing heavy atom: .R<ILE 140>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 144>
Added missing heavy atom: .R<ILE 144>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 164>
Added missing heavy atom: .R<ILE 164>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 170>
Added missing heavy atom: .R<ILE 170>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 173>
Added missing heavy atom: .R<ILE 173>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 179>
Added missing heavy atom: .R<ILE 179>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 185>
Added missing heavy atom: .R<ILE 185>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 203>
Added missing heavy atom: .R<ILE 203>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 217>
Added missing heavy atom: .R<ILE 217>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 219>
Added missing heavy atom: .R<ILE 219>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 224>
Added missing heavy atom: .R<ILE 224>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 241>
Added missing heavy atom: .R<ILE 241>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 259>
Added missing heavy atom: .R<ILE 259>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 260>
Added missing heavy atom: .R<ILE 260>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 266>
Added missing heavy atom: .R<ILE 266>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 274>
Added missing heavy atom: .R<ILE 274>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 289>
Added missing heavy atom: .R<ILE 289>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 309>
Added missing heavy atom: .R<ILE 309>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 310>
Added missing heavy atom: .R<ILE 310>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 323>
Added missing heavy atom: .R<ILE 323>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 325>
Added missing heavy atom: .R<ILE 325>.A<CD1 14>
Created a new atom named: OT1 within residue: .R<CMET 326>
Created a new atom named: OT2 within residue: .R<CMET 326>
Added missing heavy atom: .R<CMET 326>.A<O 17>
Added missing heavy atom: .R<CMET 326>.A<OXT 18>
total atoms in file: 35742
Leap added 2688 missing atoms according to residue templates:
35 Heavy
2653 H / lone pairs
The file contained 35 atoms not in residue templates
On 05/08/2012 09:44 PM, Benjamin D Madej wrote:
> Hi Albert,
>
> The script was designed for CHARMM-GUI pdb files. It sounds like the gromacs file has atoms that are named differently in POPE (or extra atoms?). Take a look to see which atoms still have the POPE label to see the differences.
>
> Those warnings are normal for loading PDBs with Lipid11 in leap.
>
> Best,
> Ben Madej
> _________________
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Received on Wed May 09 2012 - 02:30:04 PDT
