[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
> --
> 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-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list