AMBER Archive (2009)

Subject: Re: [AMBER] Building atom and angle parameters

From: George Tzotzos (gtzotzos_at_mac.com)
Date: Tue Jan 27 2009 - 12:24:52 CST

 Hi everybody,

I'm unable to save protein parameters. On

> protein = loadmol2 <myprotein.mol2
> saveamberparm protein protein.prmtop protein.inpcrd

The program aborts giving:
For atom: .R<THR3 1>.A<N 1> Could not find type: N.pl3
For atom: .R<THR3 1>.A<CA 2> Could not find type: C.3
For atom: .R<THR3 1>.A<C 3> Could not find type: C.2
For atom: .R<THR3 1>.A<O 4> Could not find type: O.2
For atom: .R<THR3 1>.A<CB 5> Could not find type: C.3
For atom: .R<THR3 1>.A<OG1 6> Could not find type: O.3
For atom: .R<THR3 1>.A<CG2 7> Could not find type: C.3
For atom: .R<PRO4 2>.A<N 1> Could not find type: N.am
For atom: .R<PRO4 2>.A<CA 2> Could not find type: C.3
etc, etc.

Any ideas? Many thanks in advance

George

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