Phosphoserine simulation using Gromacs

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Martin Klvana

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.

Marzieh Dehghan

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

Hamid Mosaddeghi

please upload your file and error. what is your force field?

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.

Vikas Dubey

Hi,

If the issue is not already resolved, I could possibly help you, if you could share your force-field and input files.