AMBER Archive (2009)

Subject: RE: [AMBER] Re: AMBER: ligand parameter

From: Ross Walker (
Date: Tue Jan 06 2009 - 22:25:20 CST

Hi Bo,

> I extract the ligand pdb from the crystal structure, and fed them to
> antechamber.
> With the .prep files, I manually changed the "DU" to the atomtype based on
> .gaff file, and use the modified .prep file to generate .parm files

What do you mean by this step: 'I manually changed the "DU" to the

You shouldn't have to change anything in the prep file and I suspect this
might be part of your problem since it is probably adding additional atoms
that shouldn't be there. Do you mean the DU's in the following type of file:

   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 C2 ca M 3 2 1 1.540 111.208 180.000 -0.17826
   5 C1 ca M 4 3 2 1.386 86.897 -162.979 -0.04968

If so you should not mess with these they are used to define the z-matrix
that describes the structure of the custom residue. Did you follow the
procedure described here: ?

> With the three ligands and FAD only, amber complains the same bond
> problems.
> I notice that when I load the protein, amber add some atoms. When I try to
> save amberparm, it complains the bond problems with these added atoms. At
> the end, the parm was created and saved.

You are getting a parm and inpcrd file but it won't be of any use due to the
long bonds. The problem is almost certainly in the prep files. If you can
send one of them it would help but I would start by making sure you follow
the procedure as described in the tutorial (and don't edit the resulting
prep file you shouldn't need to).

Grep out each residue in turn from the protein pdb file and use this single
residue pdb as the input to antechamber.
> It seems that the bond problem is associated to the atoms that are added
> by
> amber. Should the warning be ignored? As the parm files are created and
> saved at the end.

No it should not be ignored... As soon as you try to do MD you system will
blow up due to the huge bond energies you will get.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

AMBER mailing list