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