[gmx-users] martinize.py

[shivangi nangia]

Dear gmx Users,

I am trying to use martinize.py to coarse grain a peptide.

I have tried all available versions of martinize.py, but I keep getting
errors similar to one as below:

I tried using the same .py script with one of my older successful cg
conversions and I run into the error of some unknown atoms being
encountered.

Kindly help.

INFO       MARTINIZE, script version 2.4
INFO       If you use this script please cite:
INFO       de Jong et al., J. Chem. Theory Comput., 2013,
DOI:10.1021/ct300646g
INFO       Chain termini will be charged
INFO       Residues at chain brakes will not be charged
INFO       The martini21 forcefield will be used.
INFO       Local elastic bonds will be used for extended regions.
INFO       Position restraints will be generated.
WARNING    Position restraints are only enabled if -DPOSRES is set in the
MDP file
INFO       Read input structure from file.
INFO       Input structure is a PDB file.
INFO       Found 17 chains:
INFO          1:   X (Protein), 1209 atoms in 72 residues.
INFO          2:   X (Unknown), 17 atoms in 1 residues.
INFO          3:   X (Protein), 100 atoms in 6 residues.
INFO          4:   X (Unknown), 17 atoms in 1 residues.
INFO          5:   X (Protein), 721 atoms in 44 residues.
INFO          6:   X (Unknown), 17 atoms in 1 residues.
INFO          7:   X (Protein), 168 atoms in 10 residues.
INFO          8:   X (Unknown), 17 atoms in 1 residues.
INFO          9:   X (Protein), 105 atoms in 7 residues.
INFO         10:   X (Unknown), 17 atoms in 1 residues.
INFO         11:   X (Protein), 1327 atoms in 81 residues.
INFO         12:   X (Unknown), 17 atoms in 1 residues.
INFO         13:   X (Protein), 219 atoms in 12 residues.
INFO         14:   X (Unknown), 17 atoms in 1 residues.
INFO         15:   X (Protein), 396 atoms in 28 residues.
INFO         16:   X (Unknown), 17 atoms in 1 residues.
INFO         17:   X (Protein), 1296 atoms in 77 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Removing HETATM chain X consisting of 1 residues.
INFO       Total size of the system: 337 residues.
INFO       Will read secondary structure from file (assuming DSSP output).
INFO       Writing coarse grained structure.
INFO       (Average) Secondary structure has been determined (see head of
.itp-file).
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Created coarsegrained topology
INFO       Written 9 ITP files
INFO       Output contains 9 molecules:
INFO          1->  Protein_X (chain  X)
INFO          2->  Protein_X (chain  X)
INFO          3->  Protein_X (chain  X)
INFO          4->  Protein_X (chain  X)
INFO          5->  Protein_X (chain  X)
INFO          6->  Protein_X (chain  X)
INFO          7->  Protein_X (chain  X)
INFO          8->  Protein_X (chain  X)
INFO          9->  Protein_X (chain  X)
INFO       Written topology files
INFO       Note: Cysteine bonds are 0.24 nm constraints, instead of the
published 0.39nm/5000kJ/mol.



Thanks,
sxn