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.
The error message comes from residue 22, not 44. I'm guessing there is another
chain, for which residue 22 is the C-terminus? Likely this one is missing O2.
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..."
The force field expects that all of the atoms in the residue have specific
names. Adding a hydrogen should be done automatically, from the .hdb and/or
.tdb file(s).
-Justin
Thank you in advance,
Abdullah
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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