Hello Kanika,
I beleive both Jason Swails and David Case have responded to your original email. Take a look at what they said, and follow their suggestions about working through one of Amber's tutorials concerning nonstandard molecules/residues.
Best regards,
Karl
----- Original Message -----
From: "kanika sharma" <ksharma997.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, November 6, 2013 2:19:36 PM
Subject: [AMBER] Fwd: Ligand has no type
Hello Amber Users,
Being fairly new at using Amber, 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? Is it because I define ligand by LIG but then how
else should I define it?
--
*Regards,*
*KS*
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Received on Wed Nov 06 2013 - 05:30:04 PST
