[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

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 :(

 
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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>
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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

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