Hi,
On Thu, Apr 28, 2016 at 03:52:13PM +0000, Anna Cebrian Prats wrote:
> 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
>
> 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>
...
> 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?
You did not show the first clue that something is amiss:
> loadamberprep FE+3.mol2
Loading Prep file: ./FE+3.mol2
Unexpected EOF: discarding residue (73 76 1 0 0)
Checking the tutorials, reading the manual, or searching the list (deeply)
would have lead to using loadMol2 instead of loadamberprep:
HEM = loadMol2 FE+3.mol2
scott
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Received on Thu Apr 28 2016 - 11:00:03 PDT
