Good evenning
I am already working with a protein that have a ligand and a heme cofactor.
I prepared separate either the ligand and the heme group , in order to obtain the prep and parm files.
The Heme group I only have the mol2 file and the frcmod. ( I added in this email the corresponding files).
Then, I try to generate the .top and .crd files with tleap, like this:
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams FE+3.frcmod
> loadamberprep FE+3.mol2
> loadamberparams acd.frcmod
> loadamberprep acd.in
> 3hs5 = loadpdb new.pdb ( the pdb of the protein that I check it with pdb4amber)
- The pdb has to contain all (protein structure + ligand + heme group), hasn't it?
and I obtained this problems:
1) Unknown residue: HEM number: 552 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
2) Creating new UNIT for residue: HEM sequence: 553
One sided connection. Residue: missing connect0 atom.
3) Created a new atom named: FE within residue: .R<HEM 553>
Created a new atom named: CHA within residue: .R<HEM 553>
Created a new atom named: CHB within residue: .R<HEM 553>
Created a new atom named: CHC within residue: .R<HEM 553>
Created a new atom named: CHD within residue: .R<HEM 553>
Created a new atom named: NA within residue: .R<HEM 553>
Created a new atom named: C1A within residue: .R<HEM 553>
Created a new atom named: C2A within residue: .R<HEM 553>
Created a new atom named: C3A within residue: .R<HEM 553>
Created a new atom named: C4A within residue: .R<HEM 553>
Created a new atom named: CMA within residue: .R<HEM 553>
Created a new atom named: CAA within residue: .R<HEM 553>
Created a new atom named: CBA within residue: .R<HEM 553>
Created a new atom named: CGA within residue: .R<HEM 553>
Created a new atom named: O1A within residue: .R<HEM 553>
Created a new atom named: O2A within residue: .R<HEM 553>
Created a new atom named: NB within residue: .R<HEM 553>
Created a new atom named: C1B within residue: .R<HEM 553>
Created a new atom named: C2B within residue: .R<HEM 553>
Created a new atom named: C3B within residue: .R<HEM 553>
Created a new atom named: C4B within residue: .R<HEM 553>
Created a new atom named: CMB within residue: .R<HEM 553>
Created a new atom named: CAB within residue: .R<HEM 553>
Created a new atom named: CBB within residue: .R<HEM 553>
Created a new atom named: NC within residue: .R<HEM 553>
Created a new atom named: C1C within residue: .R<HEM 553>
Created a new atom named: C2C within residue: .R<HEM 553>
Created a new atom named: C3C within residue: .R<HEM 553>
Created a new atom named: C4C within residue: .R<HEM 553>
Created a new atom named: CMC within residue: .R<HEM 553>
Created a new atom named: CAC within residue: .R<HEM 553>
Created a new atom named: CBC within residue: .R<HEM 553>
Created a new atom named: ND within residue: .R<HEM 553>
Created a new atom named: C1D within residue: .R<HEM 553>
Created a new atom named: C2D within residue: .R<HEM 553>
Created a new atom named: C3D within residue: .R<HEM 553>
Created a new atom named: C4D within residue: .R<HEM 553>
Created a new atom named: CMD within residue: .R<HEM 553>
Created a new atom named: CAD within residue: .R<HEM 553>
Created a new atom named: CBD within residue: .R<HEM 553>
Created a new atom named: CGD within residue: .R<HEM 553>
Created a new atom named: O1D within residue: .R<HEM 553>
Created a new atom named: O2D within residue: .R<HEM 553>
total atoms in file: 4493
Leap added 4450 missing atoms according to residue templates:
45 Heavy
4405 H / lone pairs
The file contained 43 atoms not in residue templates
One sided connection. Residue: missing connect0 atom.
Why appears all this problems if I enter the prep and parm files?? I know that .mol2 file is not correct , but if i change it to .prep or .in, the Fe atom disappears.
How can I read the mol2 information of Heme group and used to determine structure in the pdb?
Thank you in advanced for your help
Sincerely,
Anna
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Received on Thu Apr 28 2016 - 09:00:03 PDT
