[gmx-users] Problem regarding Complex ion addition by genbox

[chris.neale at utoronto.ca]

> Thanks a lotfor responding me.Sorry for complexity.
> As you have suggest that in step 2.
> (2. Use editconf to put your guanidinium ion in a box of such a size so)>
>
>  In input X.gro file in editconf there will be one guanidium ion or total
> number of guanidium ion that is required for desired concentration.
>  How many guanidinium ion we will put in box & How to generate input .gro
> file in editconf in step 2 of your's siggested step.?

That is up to you. Read about genbox and you will see that you could  
go either route if you wanted. The method that I suggested was for a  
single ion in a box. Try that. Go ahead and use genconf if you want,  
but that would be outside of what I have suggested. If you have  
difficulty then make a test system with no protein, just an empty box  
of desired size to start, and go through the procedure that I outlined  
to see how it works.

Chris.

>
>  I have used genconf in that i used to give X.gro file contaning
> information of one molecule.It multiplies a given coordinates file.Will
> this help or which is most appropriate way to generate input .gro file
> in editconf in step 2?
>
>  In step 4 it will add water molecule according to box size.How we will
> control it for desired concentration.

>> that it is at the desired concentration (guanidinium.gro).

>> Thanks for giving me insight. But i have a query.
>> I tried to add complex ion by genion but while adding, it replaces the
>> water molecule according to my choice but it shows information of one
>> atom
>> only not of all atom of that complex molecule in structure file (.gro).i
>> then tried to use by genbox.How should it will display information of
>> all
>> atom of complex molecule ?
>
> I'll do my best to answer, but if you want some better help then I am
> afraid that you need to find somebody on your end that can assist you
> in getting the question across in english that is more easily
> understood. Unfortunately I do not understand your particular question
> on this post, I only assume that you still don't have the answer.
>
> Here is what I would first think of doing (but I have never tried it).
>
> 1. Use editconf to put your protein in the box of desired size
> (protein.gro).
>
> 2. Use editconf to put your guanidinium ion in a box of such a size so
> that it is at the desired concentration (guanidinium.gro).
>
> 3. genbox -cp protein.gro -cs guanidinium.gro -o protein_guanidinium.gro
>
> 4. grnbox -cp protein_guanidinium.gro -cs tip3p.gro -o
> protein_guanidinium_tip3p.gro
>
> 5. EM
>
> 6. Posre ME
>
> 7. MD
>
> Hope it helps,
> Chris.
>
>>> I tried with genbox option with perticular concentration i.e.
>>> perticular
>>> number of each component like guanidium ion thiocynate ion & water
>>> molecule.But while doing PR(position restrain MD) it showing errors :
>>> constraints errors in algorithm shake at step 0. t=o.oo ps : water
>>> molecule starting at atom 3010 can not be settled. check for bad
>>> contacts
>>> and/or reduce the time steps.
>>
>> Quote from 'genion -h',
>> "For larger ions, e.g. sulfate we recommended to use genbox."
>>
>> If you must use genion for some reason then the only question I see is:
>> Did you do EM? If not then try that first. Also, for genion or genbox,
>> you might try simplifying your system. Take a box of water and use
>> genion to add a single guanidium. Then EM, then MD (dt=0.002). What
>> happens?
>>
>> Chris.
>>
>>> i reduced the time steps in pr.mdp from .002 to .001 ps file but again
>>> it
>>> shows the same problem. i have seen the pdb files after genbox really
>>> some
>>> close contacts between was there it means insertion of extra molecule
>>> by
>>> gen box is not proper it leads to some bad contacts.
>>>
>>> The real problem is that when performing simulation of peptide with
>>> guanidium ion , CL- , water it is showing no problem because CL- is
>>> added
>>> in genion steps. Only change in new system (guanidium ion, SCN- ,
>>> water,
>>> peptide) is of SCN-. Addition of SCN- in genbox step is creating
>>> problem.
>>> Is any other method to  perform simulation of peptide in solvent systrm
>>> (guanidium ion, SCN-, water).
>>> Please give me some insight to resolve this issue.
>>> This is pr.mdp file
>>>
>>> title               =  Nanomer                  ; a string
>>> cpp                 =  /lib/cpp                 ; c-preprocessor
>>> define              =  -DPOSRES
>>> dt                  =  0.001                    ; time step
>>> integrator          =  md
>>> tinit               =  0.0
>>> nsteps              =  100000                   ; number of steps
>>> nstcomm             =  1                        ; reset c.o.m. motion
>>> nstxout             =  500                      ; write coords
>>> nstvout             =  500                      ; write velocities
>>> nstfout             =  0
>>> nstlog              =  500                      ; print to logfile
>>> nstenergy           =  500                      ; print energies
>>> nstlist             =  10                       ; update pairlist
>>> ; Neighbour Searching
>>> ns_type             =  grid                     ; pairlist method
>>> ; Electrostatics and VdW
>>> coulombtype         =  PME
>>> vdwtype             =  shift
>>> rlist               =  1.5                      ; cut-off for ns
>>> rvdw_switch         =  0.8
>>> rvdw                =  1.4                      ; cut-off for vdw
>>> rcoulomb_switch     =  0.8
>>> rcoulomb            =  1.5                      ; cut-off for coulomb
>>> ;Temperature coupling
>>> Tcoupl              =  berendsen                ; temperature bath
>>> (yes,no)
>>> ref_t               =  298 298
>>> tc-grps             =  Protein Non-Protein
>>> tau_t               =  0.1 0.1
>>> ; Pressure coupling
>>> Pcoupl              =  no                       ; pressure bath
>>> tau_p               =  0.5
>>> compressibility     =  4.5e-5
>>> ref_p               =  1.0
>>> ; Velocity generation
>>> gen_vel             =  yes                      ; generate initial
>>> gen_temp            =  298.0                    ; initial temperature
>>> gen_seed            =  173529                   ; random seed
>>> constraints         =  all-bonds
>>> constraint_algorithm      =  shake
>>> shake_tol           = 0.0001
>>
>>
>>
>>
>>> kinshuk at chem.iitb.ac.in wrote:
>>>> Hi all,
>>>>
>>>>   I have been trying to simulate peptide in water box with guanidium
>>>> ion
>>>> &
>>>> thiocynate ion(SCN-).I tried to add these ion by genion command line
>>>> by
>>>> simply adding topology information of these ion in ions.itp of gromacs
>>>> library directory but it is not working properly it only adds one atom
>>>> by replacing water molecule it seems that genion is applicable only
>>>> for
>>>> monoatomic ion.
>>>>   If i have to do simulation with these polyatomic ions with
>>>> perticular
>>>> salt concentration how do i will perform it.
>>>>
>>> with genbox. compute number yourself.
>>>>
>>>> Kinshuk
>>>> IIT-Bombay
>>>> India
>