[gmx-users] martinize.py
Tsjerk Wassenaar
tsjerkw at gmail.com
Sun Aug 10 20:05:49 CEST 2014
Hi sxn,
I don't see any errors. Only a note and a warning. What is the error? Don't
you get a structure and/or topology? Is either of them faulty?
Cheers,
Tsjerk
On Aug 10, 2014 6:38 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
wrote:
> 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
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