[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

OK.
 PDB FILE IS AS BELOW:

HETATM    1  C   FOR     0      -0.721   1.600   1.249 
HETATM    2  O   FOR     0      -0.839   2.806   1.453 
ATOM      3  N   VAL     1      -1.227   0.728   2.125 
ATOM      4  CA  VAL     1      -1.918   1.159   3.323 
ATOM      5  C   VAL     1      -1.969   2.678   3.410 
ATOM      6  O   VAL     1      -0.931   3.335   3.447 
ATOM      7  CB  VAL     1      -1.219   0.644   4.576 
ATOM      8  CG1 VAL     1       0.208   1.178   4.618 
ATOM      9  CG2 VAL     1      -1.976   1.118   5.812 
ATOM     10  N   SER     2      -3.181   3.235   3.442 
ATOM     11  CA  SER     2      -3.363   4.671   3.524 
ATOM     12  CB  SER     2      -4.138   5.196   2.320 
ATOM     13  OG  SER     2      -4.296   6.612   2.437 
ATOM     14  C   SER     2      -4.135   5.054   4.778 
ATOM     15  O   SER     2      -5.272   4.628   4.966

 
Sincerely,
Shima


----- Original Message -----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Wednesday, June 27, 2012 9:14 PM
Subject: Re: [gmx-users] Re: pdb2gmx error



On 6/27/12 12:43 PM, Shima Arasteh wrote:
> I know that no missing atom is here.
> As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement.
> Please help me, I don't know what to do :(
>

Please copy and paste the entirety of the first three residues in your .pdb file 
so we can see what you're working with.

-Justin

>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin A. Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, June 27, 2012 8:58 PM
> Subject: Re: [gmx-users] Re: pdb2gmx error
>
>
>
> On 6/27/12 12:25 PM, Shima Arasteh wrote:
>> You mean the order of C and O should be changed in .pdb file? If yes, it didn't work!
>>
>
> The order of atoms in the .pdb file is irrelevant.  What may be the issue is
> that when pdb2gmx is reporting the error, it is printing its own internal
> residue number (i.e., the second residue in the chain) - are you missing residue
> 1?  Files downloaded from the PDB are also convenient because they report all
> missing atoms with "MISSING" entries in the header of the file.  These entries
> will indicate problems before even running pdb2gmx.
>
> -Justin
>
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: shounakb <baners4 at rpi.edu>
>> To: gmx-users at gromacs.org
>> Cc:
>> Sent: Wednesday, June 27, 2012 8:39 PM
>> Subject: [gmx-users] Re: pdb2gmx error
>>
>> Hi,
>>       C and O should go last (i.e. their atom numbers should be 14 and 15
>> respectively.
>> Hope this works!
>>
>> Regards,
>> Shounak
>>
>> Shima Arasteh wrote
>>>
>>>     Hi all,
>>>
>>> I got this error :
>>> Atom CA is used in an interaction of type improper in the topology
>>> database, but an atom of that name was not found in residue number 2.
>>> I checked the pdb file and rtp file.
>>> .rtp file:
>>> [ SER ]
>>>     [ atoms ]
>>>         N     N  -0.280     0
>>>         H     H   0.280     0
>>>        CA   CH1   0.000     1
>>>        CB   CH2   0.150     2
>>>        OG    OA  -0.548     2
>>>        HG    HO   0.398     2
>>>         C     C   0.380     3
>>>         O     O  -0.380     3
>>>
>>> .pdb file:
>>>
>>>     ATOM     10  N   SER     2      -3.181   3.235   3.442
>>> ATOM     11  CA  SER     2      -3.363   4.671   3.524
>>> ATOM     12  C   SER     2      -4.135   5.054   4.778
>>> ATOM     13  O   SER     2      -5.272   4.628   4.966
>>> ATOM     14  CB  SER     2      -4.138   5.196   2.320
>>> ATOM     15  OG  SER     2      -4.296   6.612   2.437
>>>
>>> I guess they are in agreement, so what's the problem?
>>>
>>>
>>>
>>>
>>> Sincerely,
>>> Shima
>>> --
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>>
>>
>> --
>> View this message in context: http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html
>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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>

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

Justin A. Lemkul, Ph.D.
Research Scientist
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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