>checkValidity
Determining validity of prmtop
Lipomin.top looks OK to me!
It gives this.
But when I check even the NEWPDB structure while using the antechamber I
get a frozen contact of these phosphate groups (here I am talking about the
protonated Lipopolysachharide).
In case of deprotonated the strecic slashes and repulsions would be more.
Also the forcefields that Foley has suggested, can you please send the link
of the same.
Thanks
Regards,
M.Jones
On Mon, Aug 17, 2015 at 9:00 PM, Lachele Foley <lf.list.gmail.com> wrote:
> There are force fields tuned specifically for lipids and for
> saccharides. The manual discusses them, and their use, in detail.
>
> Also... take a good look at the parm and rst files using vmd. You can
> sometimes have bad structural problems that don't show up if you only
> inspect the pdb file.
>
>
>
> On Mon, Aug 17, 2015 at 8:43 AM, Mrinda Jones <mrindajones.gmail.com>
> wrote:
> > force fields: gaff, ff99SB and ff14SB all I have used.
> >
> > Still the error exists.
> > Also I tried taking the deprotonated phosphate groups but the same output
> > file exists.
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 3.3697E+09 5.9152E+08 5.8990E+10 O2 165
> >
> > BOND = 159074.4906 ANGLE = 910.3529 DIHED =
> > 110.2631
> > VDWAALS = ************* EEL = -42313.7223 HBOND =
> > 0.0000
> > 1-4 VDW = 29.5015 1-4 EEL = -709.5993 RESTRAINT =
> > 0.0000
> >
> >
> > What do you suggest?
> >
> > Thanks.
> >
> > Regards,
> > M.Jones
> >
> >
> > On Mon, Aug 17, 2015 at 5:19 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Mon, Aug 17, 2015, Mrinda Jones wrote:
> >> >
> >> > I am trying to simulate the Lipopolysaccharide molecule of 271 atoms.
> The
> >> > initial structure was drawn and saved in the .pdb format which stays
> as
> >> the
> >> > input file for the simulation (attached herewith).
> >>
> >> What force-field are you using? The fact that you are getting large
> values
> >> for the 1-4 EEL term suggests that you may have hydroxyl hydrogens that
> >> have
> >> zero LJ parameters, and which are getting too close to other atoms.
> >>
> >> This is likely to involve the hydrogens attached to the phosphate
> oxygens.
> >> Are you sure that you want those phosphate groups to be doubly
> protonated?
> >> That would likely occur only under very acidic conditions.
> >>
> >> Even if you go back to the singly protonated versions, which should be
> >> stable
> >> under mildly acidic conditions, you probably need to use higher force
> >> constants for the phosphate group to prevent these sorts of
> instabilities
> >> (assuming the problem does lie within the phosphate groups.) See the
> >> comments
> >> in the frcmod.phosaa10 file in $AMBERHOME/dat/leap/parm.
> >>
> >> You can find out more by using the "checkValidity" command in parmed,
> using
> >> the structure after 500 steps of minimization or so.
> >>
> >> ....dac
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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Received on Wed Aug 19 2015 - 00:30:05 PDT
