Hi
Dear all
I want to simulate a protein containing phosphoserine using MD, so I place the force field into the working directory and modified all parameters such as SEP (phosphoserine) was added as Protein in the residuestypes.dat, , but I confronted the following error?
Atom N is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 1.
please let me know how to solve this problem?
best wishes
It seems that the amino-group nitrogen atom (N) of the residue number 1 is missing. To solve this problem: add the missing atom (group).
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Not a Gromacs user.
thanks a lot, but I searched on the net and I found out the mentioned error of residuetypes.dat. I introduced phosphorylated residue in the resiuetypes.dat as "Protein" but the same error was confronted.
Is the nitrogen atom (N) of the residue number 1 defined in the relevant input files?
I don't understand the concept of mentioned error:
Atom N is used in an interaction of type improper in the topology database, but an atom of that name was not found in residue number 3
Hi
I searched on the net and found out this error due to missing residues in the pdb file, but when I want to use homology modelling using modeller, I confronted this error " sequence difference between alignment and pdb" because pdb file containing phosphoserine which is different from its sequence, i.e., there is serine in its sequence file.
please let me know how to complete these missing residues?
thanks in advances
best wishes
Marzieh: Modeller does not recognize modified amino acid residues. Convert the phosphoserine to regular serine, build homology models, and convert the serine back to phosphoserine.
Marzieh: The error message, if correct, is very straightforward: the program tells you that the nitrogen atom is missing, and the error arises when the program attempts to act on something that does not exist (for acting on something that does not exist is impossible). The key part of the error message is not the action that failed, but the reason why it failed. Check the structure, add the missing atoms, or truncate the termini.
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