On Tue, 2013-11-05 at 18:57 +0100, kanika sharma wrote:
> Hello Amber Users,
>
> I used a program for docking and got a structure which I wanted to minimise
> and use further. I used leap as instructions say and looked at the file
> that said:
>
> Loading PDB file: ./Taar131u19+CadaverineGoVina1.pdb
> Unknown residue: LIG number: 341 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
>
> Creating new UNIT for residue: LIG sequence: 342
> Created a new atom named: C1 within residue: .R<LIG 342>
> Created a new atom named: C2 within residue: .R<LIG 342>
> Created a new atom named: C3 within residue: .R<LIG 342>
> Created a new atom named: N1 within residue: .R<LIG 342>
> Created a new atom named: C4 within residue: .R<LIG 342>
> Created a new atom named: C5 within residue: .R<LIG 342>
> Created a new atom named: N2 within residue: .R<LIG 342>
> total atoms in file: 2719
> Leap added 2723 missing atoms according to residue templates:
> 2723 H / lone pairs
> The file contained 7 atoms not in residue templates
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
> FATAL: Atom .R<LIG 342>.A<C1 1> does not have a type.
> FATAL: Atom .R<LIG 342>.A<C2 2> does not have a type.
> FATAL: Atom .R<LIG 342>.A<C3 3> does not have a type.
> FATAL: Atom .R<LIG 342>.A<N1 4> does not have a type.
> FATAL: Atom .R<LIG 342>.A<C4 5> does not have a type.
> FATAL: Atom .R<LIG 342>.A<C5 6> does not have a type.
> FATAL: Atom .R<LIG 342>.A<N2 7> does not have a type.
> Failed to generate parameters
> Parameter file was not saved.
>
> How can I resolve this?
You need to create a library file (mol2 or OFF file) for your ligand and
provide that file to tleap (via the "loadMol2" or "loadOFF" commands).
See
http://ambermd.org/tutorials/basic/tutorial4b/ for more detailed
instructions.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 05 2013 - 12:30:04 PST
