FAQs

Under Construction

Here is a list of frequently asked questions. If you cannot find your question here, simply raise an issue for further help. If you can find your issue here but cannot resolve it using the answers raise an issue with the tag FAQ.

Q: Why is my structure generation slow?
A: It could be that the target density is too high for efficient packing or the random-walk gets trapped. Try decreasing the density or increasing the maximum force (-mf).

Q: Why do I get infinities in the energy minimization?
A: This means that after backmapping to target resolution two beads/atoms are overlapping. To resolve this problem try to create a system at lower target density, or reduce the maximum force allowed in the random walk (i.e. set a lower value using -mf), or try to minimize using thermodynamic integration.

Q: Why does my link not apply?
A: There are many reasons but typically it is, because the algorithm cannot find matching atoms or the link at residue level does not match any fragment in the target graph. To resolve this problem run gen_itp with the -vv flag. This will print why links don't apply. Another typically encountered problem is that for exclusions, pairs, virtual-sites, and improper dihedral angles you will have to provide an [edge] directive describing, how the fragment looks like that these interactions correspond to. In this case consult the tutorial on writing ff-files for more information.

Q: I cannot run the package, because of a 'wrapper' error?
A: This typically occurs because the numba version installed on the machine is too old. Try reinstalling numba to the most recent version.

Q: How do I include a starting structure?
A: Starting structures can be provided with the '-c' option. Note that the starting structure coordinates are associated to the first N atoms in your topology file. If you want extend some existing molecules by polymers use the '-res' flag to tell polyply that all residues with the name mentioned there have to be built. In that case all other coordinates are considered provided with the -c option. Again the order in the coordinate file needs to match the order of all other coordinates in the topology file.

Q: How do I install polyply?
A: We recommend installing polyply in a virtual environment (). In that case simply create a new environment and use 'pip install polyply'. if you are working with conda check out the conda install instructions here on the wiki. Note installing numba with polyply gives great speed ups.

Q: How do I install the development version?
A: To install the development version use: pip install git+https://github.com/marrink-lab/polyply_1.0.git#polyply_1.0