[gmx-users] Hydroixde Ion
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 22 21:16:12 CET 2011
SHIVANGI NANGIA wrote:
> Hi,
>
> Thanks so much for the prompt help.
>
> Yes, I did realize that methanol as solvent was not updated in the .top
> file. I had to fix the .top file manually.
>
> When I add ions using genion I replace methanol.
>
> As a test I tried setting up the whole system with the change that
> instead of 8 hydroxide ions I added 8 chloride ions.
> And everything works perfectly!
>
> So, I think its something with the hyrdroxide ion.
>
> I will try adding hydroxide ions using genbox.
> I think then I need to treat it as a charged residue and have it
> included in the .rtp file, correct?
>
No. Only pdb2gmx uses .rtp entries for polymeric materials (i.e. proteins and
nucleic acids). You already have a topology written for hydroxide, from what
you've shown. All you need to do is #include "hydroxide.itp" in your .top and
add the 8 required molecules with genbox -ci -nmol.
-Justin
> Thanks,
> Shivangi
>
> Shivangi Nangia
> Garrison Group
> Graduate Student
> 201A Chemistry Building
> University Park PA 16802
>
>
> 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.
> >&nbs! p; >
> > > 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&n! bsp; -1.41000 0
> >&nb! sp; > > 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 a! n 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 al! so the
> topol.top but when I try to minimize the system using>&n bsp; > >
> 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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>
--
========================================
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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