On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:
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
That's only useful for pdb2gmx when generating .top files.
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!)
Don't. The .atp defines *atom* types.
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
Use two atoms, like you did for your .rtp entry.
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.
Your .top still does not have a functional [ moleculetype ] OH. You're
probably not using the #include "ions.itp" mechanism correctly.
Mark
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