Hello, I am new gromacs user. I am trying to set up a water-methanol system with few hyrdroxide ions.
Since hyrdroxide ion does not already exist in gromacs database, I defined the following in the .rtp file ( I am using ffG53a6) [ OH ] [ atoms ] OW OW -1.41000 0 HW1 H 0.41000 0 [ bonds ] OW HW1 gb_38 [ angles ] ; ai aj ak gromos typpe [ impropers ] ; ai aj ak al gromos type [ dihedrals ] ; ai aj ak al gromos type I also included OH in the .atp file ( I realise that hydroxide ion is NOT an atom, its a diatomic anion, I was just trying!) I ran into the error: No such moleculetype OH I further included information in the ions.itp as follows: [ moleculetype ] ; molname nrexcl OH 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 OH 1 OH OH 1 -1 The genion adds the "OH" in the .gro file and also the topol.top but when I try to minimize the system using grompp -f minim.mdp -c 5his8_meohi_wat.gro -p topol.top -o em.tpr I am still running into the same error, No such moleculetype OH. Any help will be greatly appreciated to help me understand. Thanks, Shivangi Shivangi Nangia Garrison Group Graduate Student 201A Chemistry Building University Park PA 16802
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