AMBER Archive (2008)

Subject: RE: AMBER: error message of xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 30 2008 - 23:09:47 CDT

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,

Ross

 

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Catein Catherine
Sent: Thursday, October 30, 2008 8:41 PM
To: amber_at_scripps.edu
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
thanks.
> >
> > Best regards,
> >
> > patd.
> > _________________________________________________________________
> > Explore the seven wonders of the world
> > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
> > --_fd0a9266-8e69-456f-bdf8-0ca4996fab34_
> > Content-Type: text/html; charset="big5"
> > Content-Transfer-Encoding: 8bit
> > > > <html>
> > <head>
> > <sty le>
> > .hmmessage P
> > {
> > margin:0px;
> > padding:0px
> > }
> > body.hmmessage
> > {
> > font-size: 10pt;
>
> ...etc
>
>
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