GROMACS version: 2018.1
GROMACS modification: Yes/No
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:
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:
ACCSDRRCRWRCX [modified] where X is the NH2 group.
the pdb file registers the NH2 group as HETATM
Thank you. I tried using the -ter option in topology generation , with [None] for the C-terminal. It returned with this error:
Atom N1 in residue NH2 13 was not found in rtp entry NH2 with 3 atoms
while sorting atoms.
I am using the modified polypeptide pdb file. here is the link to the pdb file
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.
@mneilg, Two corrections required:
- As Justin mentioned, atom naming in PDB file should match with rtp file for NH2. For example, N instead of N1, check for hydrogens (sample below)
- Define NH2 as atom instead of heteroatom
After changing the above two, use -ter and select None