AMBER Archive (2008)

Subject: RE: AMBER: error message of xleap

From: Catein Catherine (
Date: Mon Nov 03 2008 - 03:52:24 CST

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?

From: amber_at_scripps.eduSubject: RE: AMBER: error message of xleapDate: 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 CatherineSent: Thursday, October 30, 2008 8:41 PMTo: amber_at_scripps.eduSubject: 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> >> > --_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> > > Hello,> > Only subscribers can post to the Amber List. To subscribe, send email to> containing the message body:> > subscribe amber> > After the subscription Welcome message, please resend your email to>> > Sincerely,> Amber Admin> > > Also, please post as text-only, not text + html...thanks!> > -- > David A. Case> For the Amber Development Team> email:

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