[gmx-users] Re: pdb2gmx error

Wed Jun 27 19:12:55 CEST 2012

Hi,
   removing the HETATMs worked for me when i used AMBER99SB's rtp file.
What force field are you using? Have you added the FOR topology manually (I
know this is besides the point about the problem with serine) AMBER99SB
seemed to only have topology for acetate [ACE]
I am also learning through this.
Sincerely,
Shounak

Shima Arasteh wrote
> 
> 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 &lt;jalemkul@&gt;
> To: Discussion list for GROMACS users &lt;gmx-users@&gt;
> 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 &lt;jalemkul@&gt;
>> To: Shima Arasteh &lt;shima_arasteh2001@&gt;; Discussion list for GROMACS
>> users &lt;gmx-users@&gt;
>> 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 &lt;baners4@&gt;
>>> To: gmx-users@
>>> 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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>>
> 
> -- 
> ========================================
> 
> 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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