[gmx-users] naive question about the c-terminus
abdullah_renk_ahmed at hotmail.com
Mon May 10 16:12:22 CEST 2010
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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