Re: [AMBER] Defining new atoms in AMBER

From: Kolattukudy P. Santo <>
Date: Thu, 2 Jul 2020 16:18:28 -0400

Dear Prof. Case.
I am trying to model an octahedral zinc coordination model - with four
water occupying the coordination cites modeled as in the 'bonded' model and
the rest two cites as dummy atoms available for ligands as in the cationic
dummy atom (CADA)model.
I defined oxygens (DO), hydrogens(DH), dummy atoms(DZ) and the central
zinc(ZO) as new atoms in xleap and created lib files. The frcmod files
created with TIP3P parameters for water and CADA parameters for Zinc and
The error is:
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./
Loading library: ./zob.lib
Loading parameters: ./frcmod.zob
Reading force field modification type file (frcmod)
Reading title:
Amber Force Field parameters hydrated Zinc-octahedral hybrid model-KP Santo
Loading PDB file: ./zoct.pdb
  Added missing heavy atom: .R<ZOB 5>.A<DO4 1>
  Added missing heavy atom: .R<ZOB 2>.A<DO1 1>
  Added missing heavy atom: .R<ZOB 3>.A<DO2 1>
  Added missing heavy atom: .R<ZOB 13>.A<DH8 1>

/users/santo_rug_15/amber18/bin/teLeap: Error!
Comparing atoms
        .R<ZOB 1>.A<ZO 1>,
        .R<ZOB 2>.A<DO1 1>,
        .R<ZOB 3>.A<DO2 1>, and
        .R<ZOB 12>.A<DH7 1>
       to atoms
        .R<ZOB 13>.A<DH8 1>,
        .R<ZOB 3>.A<DO2 1>,
        .R<ZOB 12>.A<DH7 1>, and
        .R<ZOB 1>.A<ZO 1>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named DH8 from ZOB did not match !

On Thu, 2 Jul 2020 at 13:20, David A Case <> wrote:

> On Thu, Jul 02, 2020, Kolattukudy P. Santo wrote:
> >I am a trying to model a compound with new atomtypes. I have prepared the
> >frcmod file and a lib file using Xleap. But with new atom types it is
> >giving me several errors.
> We need to know details: just saying that is "giving me several
> errors" doesn't provide much for us to go on.
> >Is it really possible to define new atom types and create lib files
> using
> >xleap?
> You can create the lib files with LEaP, but you also need to use
> addAtomTypes{} when you want to load these in, and well as to define the
> masses for force field parameters (etc.) of the new types in a frcmod
> file. Forgetting the addAtomTypes step is a common (and understandable)
> omission, but I'm really guessing here. Look at the leaprc files in
> $AMBERHOME/dat/leap/cmd for examples of the syntax that is needed.
> ....hope this helps....dac
> _______________________________________________
> AMBER mailing list

KP Santo
Dr. Kolattukudy P.  Santo
Post doctoral Associate
Department of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
New Brunswick, New jersey
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Received on Thu Jul 02 2020 - 13:30:02 PDT
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