[gmx-users] martinize.py

[Tsjerk Wassenaar]

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
>> --
>> 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.
>>
>