[gmx-users] naive question about the c-terminus

[XAvier Periole]

On May 10, 2010, at 4:12 PM, abdullah ahmed wrote:

> Hello everyone!
>
> I have a naive question and I have been trying to find a solution  
> myself, but I just don't understand what is wrong.
>
> When I run pdb2gmx with "-ter" on my molecule I get the following  
> error message when I ask for a COOH to be made at the C terminus (I  
> get no error when I ask for COO- ):
>
> Atom O2 not found in residue 22 while adding improper.
>
> However, My PDB file ends with:
> ATOM    282  C   LEU B  44      -5.138 -16.681   4.219  1.00   
> 0.00      B1   C
> ATOM    283  O1  LEU B  44      -4.407 -17.877   3.685  1.00   
> 0.00      B1   O
> ATOM    284  O2  LEU B  44      -6.471 -16.388   3.597  1.00   
> 0.00      B1   O
> TER     286      LEU B  44
>
> Therefore, the O2 atom is clearly there.
in residue 44!
Would you be working with a dimer ?
>
> I considered the idea that the error was because there is no  
> Hydrogen at the end of the PDB file to make the H in COOH. So I used  
> ZZ vega to add a hydrogen to O2. When this did not work I tried  
> adding one to O1, but I kept getting the following error:
> "Atom H1 in residue 22 not found in rtp entry with 19 atoms..."
>
> Thank you in advance,
> Abdullah
>
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