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

From: Richard Tseng <richard617.gmail.com>
Date: Fri, 27 Mar 2009 22:08:34 +0000

Sorry forgot to attach files

On Fri, Mar 27, 2009 at 3:51 PM, Richard Tseng <richard617.gmail.com> wrote:
> 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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>>
>



--
Chih-Yuan Tseng (Richard)
Postdoctoral fellow,
Department of Oncology
University of Alberta
Cross Cancer Institute
Edmonton, AB T6G 1Z2 Canada
Office: Sun life building 14Fl
Office phone no.: 1-780-6434440
Cell: 1-780-9082104
Email: chih-yuan.tseng.ualberta.ca; richard617.gmail.com
Homepage: http://richardcyt.myweb.hinet.net/
-----------------------------------------------------------


Received on Sun Mar 29 2009 - 01:11:15 PDT
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