AMBER Archive (2008)

Subject: RE: AMBER: error message of xleap

From: Ross Walker (
Date: Mon Nov 03 2008 - 11:05:54 CST

Hi Catein,


See $AMBERHOME/dat/leap/parm/parm99.dat


This contains all the atoms type, bonds angles etc for the FF99 force field.
This forms the basis of FF99SB / FF03 etc which just modify certain
parameters - see $AMBERHOME/dat/leap/parm/frcmod.ff99SB for example. In this
case only dihedrals containing C,N,CT and C are changed - everything else
remains at FF99.


Although just taking a look there does not appear to be any C1 or N1 atoms
types in the FF99 force field so I'm not sure where you are getting these
atoms types from. They could be gaff atom types but then they should be in
lower case. E.g. from line 160 of $AMBERHOME/dat/leap/parm/gaff.dat


c1-n1 1014.5 1.138 SOURCE1 170 0.0038 0.0055


All the best



From: [] On Behalf Of
Catein Catherine
Sent: Monday, November 03, 2008 1:52 AM
Subject: RE: AMBER: error message of xleap


Dear Ross,
Thank you very much for your help. I would like to reset the atom types for
the system. In (X-C1-N1-C3) system, X is a transition metal, there is a
triple bond between C1 and N1, while C1 and N1 are charged negatively and
positively, respectively. I understand that C1 is different from the normal
C1 as it bind with X in this complex. While the N1 is also different from
the normal N1 type, as it carry a positive one charge, with one triple bond
and one single bond.
As a start, I could like to borrow the atom types of the normal C1 and N1 to
my system, which I will redefine it as C1' and N1'. I am writing to ask
where can I found the original setting for normal C1 and N1 atom types using
in AMBER. So that I can copy them to the frcmod files for startup.
Could you mind to help?


Subject: RE: AMBER: error message of xleap
Date: Thu, 30 Oct 2008 21:09:47 -0700

Hi Catein,


X is reserved for use as a wild card in dihedral restraints so you are
probably getting a very weird set of dihedrals for your whole molecule. I
suggest you recreate your atom X and call it something else.


As for connect1 and connect0 these refer to the head and tail of the amino
acid residues, if your new residue is a nonbonded ligand then you don't need
to worry. If it is part of the protein chain then you will need to define
the head and tail or it won't get bonded into the protein chain.


Note, however, that from the error message you show the residue being
referred to has a very strange name. This would suggest that something is
wrong with your input pdb file so you might want to check this.


Good luck,




From: [] On Behalf Of
Catein Catherine
Sent: Thursday, October 30, 2008 8:41 PM
Subject: AMBER: error message of xleap


> > Dear Sir/Madam,
> >
> > I am trying to define a structure with four linear atoms (X-C1-N1-C3). I
defined atom X myself, and defined the dihedral angle as follows in the
frcmod file:
> >
> > DIHE
> > X-c1-n1-c3 1 10.00 0.000 1.00 comments
> >
> > However, when I load this frcmod file to the xleap, and generate the
prmtop and inpcrd files, the following error message appears:
> >
> > > saveamberparm x x.prmtop x.inpcrd
> > check unit
> > warning: the unperturbed charge of the unit: 1.99998 is not zero

> > --ignoring the warning.
> > Buidling topology.
> > .....
> > Building H-Bond parametrs.
> > Not Marking per-residue atom chain types.
> > Markign per-residue atom chain types.
> > (Residues lacking connect0/connect1-these don't have chain types marked:
> > res total affected
> > M! OL 1
> > )
> > (no restraints)
> >
> > Could you mind to let me know if I have define the dihedral angle
wrongly? What is the meaning of the error message (Residues lacking
connect0/connect1-these don't have chain types marked)? I used these prmtop
and inpcrd to do a short min and md calculations. However, the structures
destorted and all the energy terms becomes *****. I must have done something
wrong here, could you mind to teach me how to do make the corrections? Many
> >
> > Best regards,
> >
> > patd.
> > _________________________________________________________________
> > Explore the seven wonders of the world
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> > <head>
> > <sty le>
> > .hmmessage P
> > {
> > margin:0px;
> > padding:0px
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> > body.hmmessage
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