AMBER Archive (2009)

Subject: Re: [AMBER] Trouble saving amberparm files

From: Alison Saunders (alison.m.saunders_at_gmail.com)
Date: Mon Jul 13 2009 - 16:06:12 CDT

I did specify a force field: ff99.

On Mon, Jul 13, 2009 at 1:16 PM, Tom Joseph <ttjoseph_at_gmail.com> wrote:

> Did you specify a force field when invoking leap?
>
> --Tom
>
> > Hello,
> >
> > Here is part of my pdb file:
> - snip! -
> >
> >
> > I added Na+ ions in xleap to neautralize it, and I used solvatebox to put
> it
> > in water. My trouble comes when I try to saveamberparm. I get the errors:
> >
> >
> >
> > FATAL: Atom .R<NMET 0>.A<HN 20> does not have a type.
> > FATAL: Atom .R<NMET 0>.A<HB1 21> does not have a type.
> > FATAL: Atom .R<NMET 0>.A<HG1 22> does not have a type.
> > FATAL: Atom .R<GLN 1>.A<HN 18> does not have a type.
> > FATAL: Atom .R<GLN 1>.A<HB1 19> does not have a type.
> > FATAL: Atom .R<GLN 1>.A<HG1 20> does not have a type.
> > FATAL: Atom .R<ALA 2>.A<HN 11> does not have a type.
> > FATAL: Atom .R<MET 3>.A<HN 18> does not have a type.
> > FATAL: Atom .R<MET 3>.A<HB1 19> does not have a type.
> > FATAL: Atom .R<MET 3>.A<HG1 20> does not have a type.
> > FATAL: Atom .R<ILE 4>.A<HN 20> does not have a type.
> > FATAL: Atom .R<ILE 4>.A<HG11 21> does not have a type.
> > FATAL: Atom .R<ALA 5>.A<HN 11> does not have a type.
> > FATAL: Atom .R<VAL 6>.A<HN 17> does not have a type.
> > FATAL: Atom .R<ALA 7>.A<HN 11> does not have a type.
> > FATAL: Atom .R<SER 8>.A<HN 12> does not have a type.
> > FATAL: Atom .R<SER 8>.A<HB1 13> does not have a type.
> > FATAL: Atom .R<GLN 9>.A<HN 18> does not have a type.
> > FATAL: Atom .R<GLN 9>.A<HB1 19> does not have a type.
> > FATAL: Atom .R<GLN 9>.A<HG1 20> does not have a type.
> > FATAL: Atom .R<ILE 10>.A<HN 20> does not have a type.
> > FATAL: Atom .R<ILE 10>.A<HG11 21> does not have a type.
> > FATAL: Atom .R<SER 11>.A<HN 12> does not have a type.
> > FATAL: Atom .R<SER 11>.A<HB1 13> does not have a type.
> > FATAL: Atom .R<PRO 12>.A<HB1 15> does not have a type.
> >
> > etc. etc.
> >
> > Any ideas on how to fix this problem?
> >
> > Thanks!
> > Alison Saunders
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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