The User.mol2 file comprises of three residues which were not there in the
force field and i have loaded the library file. This mol2 file i have
generated using DBT(Dendrimer builder toolkit) so this mol2 file comprises
of three residue connected to each other. After this i have generated a pdb
solvating this molecule using packmol then for generation of top and crd in
amber i have used packmol generated pdb file Now to generated prmtop i need
to load this pdb so in amber it is not being taken as whole molecule (which
was initially present as USER.mol2 and now it has BMI as well Cl ions),
that is due to the absence of whole unit of molecule in amber. Here i can
only load lib file having info of three residues, thats why bonds are not
connected here.
I have added BMI ions using addions command.
On 11 December 2017 at 18:35, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > i need to again save the topology file which creates another problem
> because G3 molecule comprises of three residues and bonds between those
> residues are not connected now.
>
> Did you break those bonds? Were they ever there in the first place? This
> seems unrelated to your other issues. Do not trust viewers to show you
> the bonds unless they read the prmtop.
>
> > So to avoid this i have added 80 ions of BMI but then minimisation of
> solvent gives the error.
>
> How did you add the BMI?
>
> > minimisation of solvent gives the error.
>
> Sounds like you have homework to do.
>
> Bill
>
> On 12/11/17 4:20 AM, Shilpa Gupta wrote:
> > I have generated ionicbox with 300 BMI cations and 300 Chloride anions.
> Now
> > i have solvated the molecule using following scritp
> > source leaprc.gaff
> > loadamberparams frcmod.bmi
> > G3=loadmol2 USER.mol2
> > BMI = loadmol2 bmi.mol2
> > Cl = loadmol2 cl.mol2
> > ionicbox=loadpdb ionicbox.pdb
> > solvatebox G3 ionicbox 10.0
> > saveamberparm G3 ionicbox.prmtop ionicbox.inpcrd
> >
> > By this method G3 molecule solvated by 200 BMI(cations) and 280
> Cl(anions)
> > and if i am deleting the extra chloride ions then i need to again save
> the
> > topology file which creates another problem because G3 molecule comprises
> > of three residues and bonds between those residues are not connected
> now.
> > So to avoid this i have added 80 ions of BMI but then minimisation of
> > solvent gives the error.
> >
> > On 11 December 2017 at 12:12, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> You could do the solvation, then add the balancing ions manually, e.g.
> >> by replacing solvent, editing the pdb (delete all but one atom of a
> >> solvent residue, and change its residue/atom names to the desired ion).
> >> Then equilibrate to forget your sins, and let the science begin! :-)
> >>
> >> Bill
> >>
> >>
> >> On 12/10/17 10:09 PM, Shilpa Gupta wrote:
> >>> Since the solvent pdb has cations as well anions therefore with loadpdb
> >>> command solvent is being added but in unequal number (randomly), and i
> >> want
> >>> equal number of cations and anions.
> >>>
> >>>
> >>> On 11 December 2017 at 11:35, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>
> >>>> <ignore>You have to manually re-type the pdb file for it to work
> >>>> :-)</ignore>
> >>>>
> >>>> Try loading the box with loadpdb, then use it like you'd use any other
> >> box.
> >>>> Bill
> >>>>
> >>>>
> >>>> On 12/10/17 8:37 PM, Shilpa Gupta wrote:
> >>>>> Dear Amber Users,
> >>>>> I want to know that how can i solvate the molecule in amber, if the
> >>>> solvent
> >>>>> box i have generated using packmol rather than creating the whole
> >>>> solvated
> >>>>> system in packmol.
> >>>>>
> >>>>>
> >>>>> Shilpa
> >>>>> _______________________________________________
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> >>
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Received on Mon Dec 11 2017 - 05:30:02 PST
