AMBER Archive (2009)

Subject: Re: [AMBER] Trouble saving amberparm files

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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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