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

[Justin A. Lemkul]

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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-- 
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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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