I'm trying to simulate the binding site of a short 6 amino acid long
peptide and a Cu2+ ion
I'm not entirely sure if my process is right
but basically I
1. Used Gaussian09 and Gauss View to build the molecule
2. Saved as mol2,
3. Opened the mol2 file with Spartan to be able to save it as a pdb file
4. Modified the PDB file by hand, labelling atom names and residues,
deleting hydrogen atoms
5. Open xleap
source leaprc.protein.ff14SB
loadoff atomic_ions.lib
loadamberparams frcmod.ions234lm_1264_spce
then load the pdb file
assign a 2+ charge to the Cu atom
add a bond between a single oxygen atom in the third residue and the Cu atom
and then tried to saveamberparm.
I get this from leap.log
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: O - Cu2+
Building angle parameters.
Could not find angle parameter: C - O - Cu2+
Building proper torsion parameters.
Building improper torsion parameters.
total 27 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
Why does it not save?
I tried using antechamber to generate a pdb file from the mol2 file, but
the resulting pdb file doesn't have any charges, and saveamberparm dosent
work because the atoms don't have any types
WARNING: There is a bond of 4.339844 angstroms between:
------- .R<MOL 114>.A<Cu1 1> and .R<MOL 114>.A<O28 28>
FATAL: Atom .R<MOL 114>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 114>.A<O3 3> does not have a type.
FATAL: Atom .R<MOL 114>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 114>.A<H5 5> does not have a type.
FATAL: Atom .R<MOL 114>.A<N6 6> does not have a type.
FATAL: Atom .R<MOL 114>.A<H7 7> does not have a type.
Do I have to manually assign types to the pdb file?
I also tried loading the mol2 file directly and that fails as well
Any help I could get would be highly appreciated. Thanks
Eugene
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Received on Tue Apr 25 2017 - 21:00:02 PDT
