Dear all,
I am using the charmm36 all atom forcefield with GROMACS 5.0 to run an MD simulation on a ~40aa peptide including one phosphorylated tyrosine. The wild-type peptide (attached here as wt_native) generates a correct topology with pdb2gmx. I used the CHARMM-GUI to generate the phosphorylated peptide PDB (Y6-2P) and modified the residue name of tyrosine for it to match the phosphotyrosine listed in the .rtp file, and gave it to pdb2gmx, which is when I encountered problems.
Pdb2gmx runs and completes but it identifies the serine preceding that phophorylated tyrosine as a C-terminal and truncates the peptide, making the simulation unuseable. If I phosphorylate the serine instead, the preceding alanine is recognized a C-terminal. The same pattern occurs with any other peptide I run, including example ones from the charmm36 paper. My installation of the force field seems correct because I am able to correctly run protonations (with PDBs edited through the charm GUI), and the force field can be used with non-post transcriptionally edited peptides and works fine.
I have not changed anything in the forcefield after downloading it, I just put the folder in my working directory and called it from there, but I still zipped it and joined it to this post as reference, as well as PDBs of my wild-type and phosphorylated peptide.
Is there a step I am missing in the force field setup ? I tried adding a .dat file to the forcefield folder but it did not seem like it was being used.
Thank you in advance.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue - you forgot step 5.
More simply, CHARMM-GUI can do everything for you, including building the entire system and writing its topology. That may be less complicated.
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue - you forgot step 5.
More simply, CHARMM-GUI can do everything for you, including building the entire system and writing its topology. That may be less complicated.
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