[gmx-users] martinize.py

[shivangi nangia]

Thanks a lot Tsjerk, it was the Histidine residue which was named HSD in
the .pdb file, on changing to HIS, the python script works.




On Sun, Aug 10, 2014 at 2:08 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Oh, maybe you mean the hetatm stuff... Every so many residues one residue
> with 17 atoms is excluded? What residue is that? I guess it's not a
> standard amino acid...
>
> Cheers,
>
> Tsjerk
> On Aug 10, 2014 8:05 PM, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
>
> > 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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