AMBER Archive (2009)

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

From: Richard Tseng (richard617_at_gmail.com)
Date: Sun Mar 29 2009 - 14:20:37 CDT

Thanks a lot!!
Since I have mixed RNA and proteins, I first
load leaprc.ff03.r1 then I load leaprc.rna.ff02.
There are no fatal error messages. However, according to
Ambertool manual suggestion the old force field is not recommended.
How about leaprc.rna.ff02?

The pdb file is directly extracted from protein data bank!!

Chih-Yuan Tseng

On Sat, Mar 28, 2009 at 7:25 AM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> 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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