Hello,
Thanks a lot for the suggestion.
I think I made some progress but I am not there yet.
I added the following in the ions.itp file
[ moleculetype ]
; molname nrexcl
OH 1
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 OH 1 OH OH 1 0
1 OW 1 OW OW 1 -1
Still I ran into the same error that it could not find moleculetype OH.
Than I specifically added the following to the .top file
[ moleculetype ]
; molname nrexcl
OH 1
[atoms]
1 OH 1 OH OH 1 0.21 1.008 ;
2 OW 1 OH OW 1 -1.21 15.99994 ;
[ bonds ]
OW HW1 gb_38
This helped.
However, there is new error I am running into which says:
Fatal error: number of coordinates in coordinate file (5his8_meohi_wat.gro,
12487) does not match topology (topol.top, 12519)
I am trying to add 8 hydroxide ions in my methanol-water system.
The confusion I have is:
The .gro file has OH but is gromacs really accounting OH as 2 atoms?
Also, the difference (12519-12487) is greater than 8.
Kindly help.
Thanks,
Shivangi
Shivangi Nangia
Garrison Group
Graduate Student
201A Chemistry Building
University Park PA 16802
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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