AMBER Archive (2009)

Subject: Re: [AMBER] Problem with "Atom does not have a type"

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Mar 28 2009 - 08:25:33 CDT

On Fri, Mar 27, 2009, Richard Tseng wrote:

> I checked again after loading leaprc.ff03.r1,

The standard leaprc files assume that nucleic acids are DNA. If you
have mixed DNA/RNA, you can't use the (old) standard PDB names (which
are ambiguous), and must use the PDB version 3 names: DA,DG,DC,DT and
RA,RU,RC,RG as residue names.

If you have all RNA, look for leaprc files with "rna" in the name.

> The leap tries to "creating atom..." when I load pdb file for single Uracil.
> Afterward, it shows "Fatal: atom does not have a type".
> Besides, for all of cases, the leap has problem in recognize
> O2'.

You have to fix this problem before you can proceed.

[Where did your files come from? I'm not familiar with using column 22
to distinguish deoxyribose from ribose...is that a standard? If so, we
should teach Amber to recognize it.]

...good luck...dac

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