pycgtool issueshttps://git.soton.ac.uk/jag1e17/pycgtool/-/issues2018-02-14T10:42:15Zhttps://git.soton.ac.uk/jag1e17/pycgtool/-/issues/18specifying bonds between 2 residues2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukspecifying bonds between 2 residues*Created by: vsbgithub*
Hello,
I am attempting to generate a CG model for a polymer using pycgtool. I have already set-up and run the atomistic system for the polymer in a solvated environment.
I was able to get the CG mapping sch...*Created by: vsbgithub*
Hello,
I am attempting to generate a CG model for a polymer using pycgtool. I have already set-up and run the atomistic system for the polymer in a solvated environment.
I was able to get the CG mapping scheme to work and generate a CG.gro file using your tool.
However, I had to specify 3 residue types in the polymer (namely start, middle and end residues). Note that each residue consists of 3 types of beads.
I had to consider 3 residues since the number of atoms on the start, middle and end residues for any polymer will be different and hence I cannot get the mapping scheme to work if I only consider a single residue type.
Since the start residue is bonded to the middle residue which in turn is bonded to the end residue, I was wondering how it'd be possible to specify this in the .bnd file. The examples all consider CG systems that only consist of 1 residue type.
How do we specify bonds between beads belonging to different residue types in pycgtool?
Would this even be possible or is it only possible to have bonds within a residue?
Thank you.
Vivek
https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/15Abstract writing of output files2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukAbstract writing of output files*Created by: jag1g13*
To allow proper testing of output files, split file writing into a separate function. Existing functions that write files should return a list of strings to pass to the file writer. Unit tests can check the list ...*Created by: jag1g13*
To allow proper testing of output files, split file writing into a separate function. Existing functions that write files should return a list of strings to pass to the file writer. Unit tests can check the list of strings more easily than a file, particularly in the case of the forcefield directory.https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/14Calculate parameters for dihedrals with multiplicity >12018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukCalculate parameters for dihedrals with multiplicity >1*Created by: jag1g13*
*Created by: jag1g13*
https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/12More warnings2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukMore warnings*Created by: jag1g13*
Warn if molecules are not mapped - catches typos in residue names in map/bnd files*Created by: jag1g13*
Warn if molecules are not mapped - catches typos in residue names in map/bnd fileshttps://git.soton.ac.uk/jag1e17/pycgtool/-/issues/10Add multiprocessing2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukAdd multiprocessing*Created by: jag1g13*
Current version is slower, though much more powerful, than the older C++ version, partly due to lack of parallelism.
*Created by: jag1g13*
Current version is slower, though much more powerful, than the older C++ version, partly due to lack of parallelism.
https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/9Make use of mdtraj.Trajectory2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukMake use of mdtraj.Trajectory*Created by: jag1g13*
Much of the file input/output could be done using mdtraj.Trajectory which would make many more file formats available. This could initially be done simply by replacing the current file IO functions, but longer ter...*Created by: jag1g13*
Much of the file input/output could be done using mdtraj.Trajectory which would make many more file formats available. This could initially be done simply by replacing the current file IO functions, but longer term mdtraj.Trajectory should allow almost complete replacement of the Frame class and a simplified process.
https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/6Create mapping files for molecules in standard MARTINI set2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukCreate mapping files for molecules in standard MARTINI set*Created by: jag1g13*
Creating mapping files for every lipid/etc in the standard MARTINI force field will allow PyCGTOOL to be used in mapping only mode to behave like MARTINIZE. The user will not be required to write a custom mapping ...*Created by: jag1g13*
Creating mapping files for every lipid/etc in the standard MARTINI force field will allow PyCGTOOL to be used in mapping only mode to behave like MARTINIZE. The user will not be required to write a custom mapping and the output GRO file will be compatible with the standard MARTINI itp.
https://git.soton.ac.uk/jag1e17/pycgtool/-/issues/5Add other output formats - LAMMPS2018-02-14T10:42:15ZJames Grahamj.graham@soton.ac.ukAdd other output formats - LAMMPS*Created by: jag1g13*
*Created by: jag1g13*