I believe this should normally produce a GoMartini model given martinize2 documentation about -govs-include. The molecule_0.itp file produced indeed includes virtual Go sites:
[ atoms ]
…
95 Q5 42 ALA BB 95 -1
96 TC3 42 ALA SC1 96 0.0
97 molecule_0_1 1 ASP CA 97 0
98 molecule_0_2 2 ALA CA 98 0
…
[ virtual_sitesn ]
; Virtual go site
97 1 1
98 1 3
99 1 5
…
However the first energy minimization (before solvation by insane.py) returns an error (in 01-TOPOLOGY-CG.log):
ERROR 1 [file molecule_0.itp, line 111]:
Atomtype molecule_0_1 not found
I believe that entering the --martinize-govs-include argument should return a warning or an error until Go̅ model are up and running with martinize2.
The subsidiary question is: using martinize2 and martini3 forcefield in martinate.sh, how should I make a Go̅-like model of my protein? What am I missing right now to get a valid topology for GROMACS? Tutorials are scarce and dedicated to martini2, but given this paper I believe it is already doable.
Using this command:
I believe this should normally produce a GoMartini model given martinize2 documentation about
-govs-include
. Themolecule_0.itp
file produced indeed includes virtual Go sites:However the first energy minimization (before solvation by
insane.py
) returns an error (in01-TOPOLOGY-CG.log
):I believe that entering the
--martinize-govs-include
argument should return a warning or an error until Go̅ model are up and running withmartinize2
.The subsidiary question is: using
martinize2
and martini3 forcefield inmartinate.sh
, how should I make a Go̅-like model of my protein? What am I missing right now to get a valid topology for GROMACS? Tutorials are scarce and dedicated to martini2, but given this paper I believe it is already doable.