Open overshiki opened 1 year ago
This certainly is an area where Molly is lacking features at the moment. In this case it looks like the atom names in the PDB file are different from those in the XML force field. Currently they have to match exactly, whereas more mature software matches residues based on topology and allows different atom names.
This issue can be left open to track this. In the mean time I would consider using OpenMM's protein preparation tools, which should match their force field file better. The system you get out won't be directly comparable to the Gromacs system, but depending on system size you may struggle to sample long enough with Molly to make a direct comparison anyway.
All of this will hopefully be fixed long term. More robust setup tools is on the todo list but not at the top.
Hi, I'm trying to use
Molly.jl
to reproduce some of the work I have done inGromacs
, however, it raises error inSystem
building stage. Specifically, I use the followingGromacs
commands to prepare the pdb file(with water box and ions):And use the following
Molly.jl
code to generate thesystem
:the
ff99SB.xml
andspce_standard.xml
files are found fromopenmm
source code.This gives me the following error:
and a lot of warning:
I know the process of combining
openmm
,Gromacs
andMolly.jl
toolchain is kind of error prone. However, sinceMolly.jl
currently does not have toolset for processing pdb files(creating water box, adding ions, etc), this is the best I come up with...Do you have any clues about what's going on here? Any suggestions on pdb preparation for
Molly.jl
?