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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
