[gmx-users] Re: pdb2gmx error

[Shima Arasteh]

You mean the order of C and O should be changed in .pdb file? If yes, it didn't work!

 
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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