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

From: Richard Tseng <>
Date: Fri, 27 Mar 2009 21:51:32 +0000


I checked again after loading leaprc.ff03.r1,
the parm99.dat and all_nucleic94.lib are loaded as well.
There is no problem of loading pdb of single Adenine, Cytosine and Guanine.
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'. Are these problems related that I does not set up
initial structure properly? How come the leap just cannot
recognize Uracil? I missed something here. Thanks!!

The attached pdb files are the four bases I extracted from protein databank.


Richard Tseng

On Fri, Mar 27, 2009 at 5:44 AM, David A. Case <> wrote:
> On Thu, Mar 26, 2009, Richard Tseng wrote:
>> I first tried to generate topology and coordinate files for the RNA
>> sequence.  After loading the corresponding pdb file into leap, there are
>> message indicates a fatal error, atom does not have a type.
> Are you sure there is not some message of the sort "creating atom...".
> Be sure that the atom names in the PDB file exactly match the atom names
> in the RNA library.  Mismatches are usually the cause of the error
> message you cite.
> ....dac
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Received on Sun Mar 29 2009 - 01:11:08 PDT
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