[gmx-users] Hydroixde Ion
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 22 20:55:23 CET 2011
SHIVANGI NANGIA wrote:
> Hi again,
>
> I have the following:
>
> I have not changed anything in ffG53a6.atp and .rtp
> As suggested by gmx users, I have 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
>
>
> I executed the following commands:
>
> (a) pdb2gmx -f his8.pdb -ignh -ter -his -p topol.top -o his8.gro
> (b) editconf -f his8.gro -box 5 5 5 -o his8box.gro
> (c) genbox -cp his8box.gro -ci 1methanol.gro -nmol 1800 -o
> his8_meoh.gro -p topol.top
Were all 1800 methanol molecules properly inserted here? Note that genbox does
not update the topology automatically for any molecules other than water.
> (d) grompp -f ions.mdp -c his8_meoh.gro -p topol.top -o ions.tpr -p
> topol.top
> (e) genion -s ions.tpr -o added_ions.gro -p topol.top -pname NA -nname
> OH -nn 8
Per the genion help information, it is not well-suited to inserting polyatomic
ions. Also, what are you choosing to replace here? genion is designed to
replace water molecules with monoatomic ions, but you haven't added any water
yet. If you're simply replacing elements of the "System" group, you've probably
got fractional species somewhere. I would be willing to bet that this process
is what is causing your problem. Check the contents of the coordinate file and
topology before and after genion, and you will probably find the problem.
Solution: don't use genion. Use genbox -ci -nmol to add your 8 OH molecules.
-Justin
> (f) genbox -cp added_ions.gro -cs tip4p.gro -o his8_meohi_wat.gro -p
> topol.top
>
> Commands (a)-(f), all goes smooth.
>
> When I do the following
> grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
>
> I run into error which says moleculetype OH not found.
>
>
> Added the following specifically in .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
>
> Going back to the command
> grompp -f minim.mdp -c his8_meohi_wat.gro -p topol.top -o em.tpr
>
> runs into different error as mentioned earlier : Fatal error: number of
> coordinates in coordinate file (5his8_meohi_wat.gro, 12487) does not
> match topology (topol.top, 12519)
>
> The .top file includes tip4p.itp, methanol.itp and ions.itp.
>
> So I am totally confused as to where I am going wrong.
> Please guide.
>
> Thanks,
> Shivangi
>
>
>
> Shivangi Nangia
> Garrison Group
> Graduate Student
> 201A Chemistry Building
> University Park PA 16802
>
> >
>
>
>
>
>
> 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.
> >
>
> And how are you attempting this? What command(s) did you give? What
> subsequent modifications to your topology did you make?
>
> The generic solution to your problem can be found here:
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> > The confusion I have is:
> > The .gro file has OH but is gromacs really accounting OH as 2 atoms?
>
> Gromacs assigns parameters to the molecules it finds based on the
> entries in the respective [moleculetypes]. If you tell grompp or any
> other program that the [moleculetype] "OH" is comprised of two atoms,
> then there's no reason to believe anything is wrong.
>
> > Also, the difference (12519-12487) is greater than 8.
> >
>
> Without some context as to what you're doing and what you've done up to
> this point, this information does not lead to any useful solution. The
> number of molecules (either methanol or OH) in your topology does not
> match the contents of your coordinate file.
>
> -Justin
>
> > 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 ]
> >&! nbsp; > ; ai aj a! k & nbsp; 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
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.beva! nlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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