mutated-godmd

Based on GOdMD (Sfriso, P, et al Bioinformatics 2013)

Code to find transition paths between two known structures mimicking the effect of mutations.

Requirements

• gfortran compiler

How to compile it

1. Modify the config.mk file. Change the variable F77 variable to point to the gfortran compiler
2. Run make clean in the main directory
3. Run make in the main directory

Input files

• -i < parameter file >
• -pdbin < initial structure in PDB format >
• -pdbtarg < target structure in PDB format >
• -p1 < alignment file, for initial structure>
• -p2 < alignment file, for target structure>
• -touch < residues to mutate >
• -ener Output, < energy file >
• -trj Output, < trajectory file >
• -o Output, < log file >

How to run it

The exe godmd file is in the ./exe directory

In the example directory run:

$ ../exe/godmd -i param.in -pdbin 1ake_A.pdb -pdbtarg 4ake_A.pdb -p1 1ake_A.aln -p2 4ake_A.aln -touch mutations.dat -trj test.trj.crd -ener test.ener.dat -o log_1ake.txt

Mutations format

33 50.

32 50.

34 50.

Should be interpreted as: Resiudes 33, 32, 34 will have they energy interactions 50 times more stable.