Dave,
Thanks!!
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.
regards,
Richard Tseng
On Fri, Mar 27, 2009 at 5:44 AM, David A. Case <case.biomaps.rutgers.edu> 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
