<div>Hello,<br><br>Thanks a lot for the suggestion.<br><br>I think I made some
progress but I am not there yet.<br><br>I added the following in the ions.itp
file<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 0<br>1 OW 1
OW OW 1 -1<br><br><br>Still I ran into the same error
that it could not find moleculetype OH.<br><br>Than I specifically added the
following to the .top file<br><br>[ moleculetype ]<br>; molname
nrexcl<br>OH 1<br><br>[atoms]<br>
1
OH 1 OH
OH 1
0.21 1.008
;<br> 2
OW 1 OH
OW 1
-1.21 15.99994 ;<br>[ bonds ]<br>
OW HW1 gb_38<br><br>This helped. <br>However,
there is new error I am running into which says: <br>Fatal error: number of
coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not match
topology (topol.top, 12519)<br><br>I am trying to add 8 hydroxide ions in my
methanol-water system.<br><br>The confusion I have is: <br>The .gro file has OH
but is gromacs really accounting OH as 2 atoms? <br>Also, the difference
(12519-12487) is greater than 8. <br><br>Kindly
help.<br><br>Thanks,<br>Shivangi<br><br><br><br>Shivangi Nangia<br>Garrison
Group<br>Graduate Student<br>201A Chemistry Building<br>University Park PA
16802<br><br>On 22/03/2011 7:44 AM, SHIVANGI NANGIA wrote:<br>>
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>That's
only useful for pdb2gmx when generating .top files.<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>Don't. The .atp
defines *atom* types.<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>Use two atoms, like you did for your .rtp
entry.<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>Your .top still
does not have a functional [ moleculetype ] OH. You're probably not
using the #include "ions.itp" mechanism
correctly.<br><br>Mark<br><br></div>