On Wed, Feb 04, 2015, Fatemeh Sadat Alavi wrote:
>
> complex = loadpdb complex.pdb
> I have error while I used atom type belong LIG.frcmod for LIG in complex.pdb
> and atom labels in the pdb file are the same labels used in my generated
> mol2 file for ligand.
> Creating new UNIT for residue: HEM sequence: 224
> Created a new atom named: Fe1 within residue: .R<HEM 224>
> ....
Just to expand: this error means that you have an atom named Fe1 in residue
HEM in you PDB file, but that atom name is not present in the library file
containing the HEM residue.
Assuming that HEM is the "LIG" you are referring to, it's not clear why
you were able to create the ligand file correctly, but not the complex file.
We don't have enough information to be of more help.
(I do note that the "ligand" residue seems to me named "MOL" in the library
file, whereas is looks like it is named "HEM" in your complex.pdb file. The
residue names in the library file and in the PDB file need to match.)
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 04 2015 - 05:00:02 PST
