[gmx-users] Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms while sorting atoms

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 1 22:17:21 CEST 2010


Nilesh Dhumal wrote:
> I have addes the "CO" residue.
> Coordinate file
> 
> REMARK   Accelrys Discovery Studio PDB file
> REMARK   Created:  Fri May 28 17:26:23 Eastern Daylight Time 2010
> HETATM    1  C1  CO     0      -1.044  -0.027   0.066  0.00  0.00           C
> HETATM    2  O2  CO     0      -0.009   0.642  -0.037  0.00  0.00           O
> HETATM    3  O3  CO     0      -2.286   0.595  -0.030  0.00  0.00           O
> END
> 
> in ffopla.rtp file.
> 
> [ CO ] ; mandatory
> [ ATOMS ] ; mandatory
>  C1   opls_974    1.00   1
>  O2   opls_975   -0.50   2
>  O3   opls_976   -0.50   2
> 
> [ bonds ]
>  C1 O2
>  C1 O3
> 
> I have also addes new atoms typs in ffopls.atp file.
> 

These input files work fine for me.  The error message complained about an atom
named "O" so be sure you're using the input you think you are.  Something has
gotten confused somewhere.

-Justin

> NIlesh
> 
> On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>>
>>>
>>> I am getting the following error during pdb2gmx.
>>>
>>>
>>> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms
>>>  while sorting atoms
>>>
>>> I checked the pdb file and ffopls.rtp file also.
>>>
>>>
>> And what did you find?  To my knowledge there is no such residue "CO" in
>> the ffoplsaa.rtp file.  Is this something you've added?  Regardless,
>> there's a mismatch somewhere, so if you can't identify it, post the text
>> of your coordinate file and the relevant .rtp entry to see if someone else
>> can spot it.
>>
>> -Justin
>>
>>
>>> Nilesh
>>>
>>>
>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>> ========================================
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> 
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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