I want to do a simulation using the OPLS-AA/L force field. However, my protein has a modified residue, an amidated C-terminal, to be exact. I modified the protein using UCSF Chimera, adding the amide group. However, I did not change the name of the residue, instead adding a new “residue” NH2 at the end.
When I tried to generate the topology file, the system returned a fatal error:
Fatal error:
atom C not found in buiding block 13NH2 while combining tdb and rtp
My question is this:
Do I need to modify the OPLS-AA/L force field to run my simulation, and if so, how?
Alternatively, what force field could I use that recognizes my modified residue?
What do you mean the modification?
If it is only the terminal NH2, you can use pdb2gmx with -ter option instead of manual modification using chimera.
Please tell all your modifications? Otherwise it is difficult to understand.
More specifically, use -ter to choose ‘None’ for the C-terminus so that pdb2gmx does not attempt to build a carboxylate onto the NH2 residue. That’s what it’s trying to do, given the error above.
I only modified the C-terminal residue, replacing the -OH group of the C-terminal aa with -NH2 using Chimera. I did not change the naming convention of the last residue such that the sequence goes like:
ACCSDRRCRWRC [unmodified]
ACCSDRRCRWRCX [modified] where X is the NH2 group.
Atom names in the coordinate file have to match what the .rtp file expects. This same issue has been discussed several times within the last day or so on this forum. Please look at the other threads (or Google) to see previous discussions.