[gmx-users] Hydroixde Ion

SHIVANGI NANGIA sxn225 at psu.edu
Mon Mar 21 21:44:50 CET 2011


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.


Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802

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