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

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Mon May 10 16:12:22 CEST 2010

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. 

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,
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