You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
The text was updated successfully, but these errors were encountered:
OLaprevote
changed the title
GoMartini produced using Martinize2 don't run on GROMACS
GoMartini topology produced using Martinize2 doesn't run on GROMACS
May 17, 2021
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.The text was updated successfully, but these errors were encountered: