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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Received on Mon Aug 17 2015 - 06:00:05 PDT
