pckroon
commented
2 years ago Hello hello,
Please note that vermouth does not support running on python2, and py2 is EOL. Please upgrade to py3.
You indeed need to add new molecules to 1) universal, 2) target ff (martini3001 in this case), and 3) the mapping between them. Since you added your new files to the py2 folder (rather than py3) it's probably not the folder the code is looking in. So please purge Python2 from your machine :) and try again
... into universal/aminoacids.rtp
You can also add them to a separate file (phospholipids, for example) if you prefer.
ELambden
Hi,
I have been attempting to coarse grain a membrane using martinize2; I have three lipids which I have charmm36 definitions for and an input .pdb file which contains the membrane. I have attempted to add in these new molecules to the force fields for martinize2 but I have been going around in circles.
In the /.local/lib/python2.7/site-packages/vermouth/data/force_fields folders, I have added in new definitions for these molecules into universal/aminoacids.rtp, and also in martini3001/martini_v3.0.0_phospholipids.itp and the same new definitions in martini3001/aminoacids.ff also as a safety measure... I have added in some LIPID.charmm36.map files whose format I believe is correct. I have these in the local directory I am running the script from and also in /.local/lib/python2.7/site-packages/vermouth/data/mappings .
I am using martinize2 in Spyder with the following flags: martinize2.py -f C:/Users/emfla/Desktop/coarsegrain/epidermicin/gramposmemb/charmm-gui-3431070502/gromacs/martini3.0/smaller_input.pdb -x input_charmm_cg.pdb -from universal -ff martini3001 -v -maxwarn 1000 -write-graph graph_out.pdb -write-repair repair_out.pdb
The write-graph output contains just the pdb file with the same molecules, although some extra bonds are unnecessarily added due to distance. The write-repair output gives me an empty file. My error message is:
WARNING - unknown-residue - vermouth.processors.repair_graph - Cannot recognize residue 'POPG' in molecule 1. Deleting the molecule.
I have used the default version of martini POPG so I am unsure why it is not recognising it. Presumably I need to add in its definition to somewhere else that I have neglected but the documentation isn't clear on where that is. Any assistance would be greatly appreciated; let me know if there's any other info needed or perhaps some files that I can provide.
If I use -list-blocks I get the following: The following Blocks are known to force field universal: ALA, ARG, ASN, ASP, ASPP, CYS, CYS2, GLN, GLU, GLUP, GLY, HSD, HSE, HSP, HIS, ILE, LEU, LYS, LSN, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, ALAD, HEME, HEO2, O2, CO, HOH, TIP3, TP3M, HO4, SOD, MG, POT, CES, CAL, CLA, ZN2, ACE, CT3 The following Modifications are known to force field universal: C-ter, COOH-ter, N-ter, NH2-ter, GLU-H, HSD, HSE, HSP, ASP0
The following Blocks are known to force field martini3001: GLY, ALA, CYS, VAL, LEU, ILE, MET, PRO, HYP, ASN, GLN, ASP, GLU, THR, SER, LYS, ARG, HIS, HIH, PHE, TYR, TRP The following Modifications are known to force field martini3001: C-ter, N-ter, COOH-ter, NH2-ter
So neither martini3001 or universal seem to have POPG & two other custom lipids in their list of blocks...