On Mon, Jan 12, 2015, 杨川 wrote:
> I have a complex that contain a ligand and MN2+ ions . I use
> Amber14 for simulation. I downloaded the parameters for MN2+ from
> http://www.pharmacy.manchester.ac.uk/bryce/amber/. I use tleap to
> make topology for complex. but when i load the complex into the tleap
> ( i also checked the xleap version) it gives the following error and
> automatically quit the tleap. Any kind of help will be appriciated.
Note that your errors have nothing to do with manganese.
>
> > com = loadpdb complex.pdb
> Loading PDB file: ./complex.pdb
> (starting new molecule for chain )
> -- residue 488: duplicate [ C] atoms (total 16)
> -- residue 488: duplicate [ F] atoms (total 2)
> -- residue 488: duplicate [ H] atoms (total 8)
> -- residue 488: duplicate [ H1] atoms (total 2)
> -- residue 488: duplicate [ H2] atoms (total 2)
> -- residue 488: duplicate [ N] atoms (total 4)
> -- residue 488: duplicate [ O] atoms (total 4)
You need to examine residue 488 in your input PDB file: why are there so many
duplicate atoms? Atom names within a residue must be unique.
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Created a new atom named: HD1 within residue: .R<HIE 293>
> Created a new atom named: HE2 within residue: .R<GLU 318>
> Created a new atom named: HD1 within residue: .R<HIE 320>
> Created a new atom named: HD1 within residue: .R<HIE 335>
> Created a new atom named: HD1 within residue: .R<HIE 341>
> Created a new atom named: HD1 within residue: .R<HIE 392>
> Created a new atom named: HD1 within residue: .R<HIE 398>
> Created a new atom named: HC within residue: .R<CASN 486>
You have atoms in your input PDB file that are not in Amber's residue
templates. You need to manually assign histidines to HIE, HID or HIP as
appropriate. It is not clear why you have an atom named "HC" in your ASN
residue...you will need to examine this.
Chapter 11 ("Preparing PDB files") in the Amber14 Reference Manual has a
discussion of steps you need to take to prepare PDB files for Amber.
...good luck...dac
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Received on Mon Jan 12 2015 - 05:30:03 PST
