AMBER Archive (2008)

Subject: AMBER: error message of xleap

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Oct 30 2008 - 22:40:49 CDT

> > 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> > MOL 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 chai!
 n 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>> > <style>> > .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> majordomo_at_scripps.edu containing the message body:> > subscribe amber> > After the subscription Welcome message, please resend your email to!
> amber_at_scripps.edu.> > Sincerely,> Amber Admin> > > Also, please post
 as text-only, not text + html...thanks!> > -- > David A. Case> For the Amber Development Team> email: amber-admin_at_biomaps.rutgers.edu
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