On Wed, Aug 19, 2015, Mrinda Jones wrote:
>
> But when I check even the NEWPDB structure while using the antechamber
I'm not sure what is in the NEWPDB file for antechamber, but what LEaP sees is
the pdb file you give it. Cooridinates in NEWPDB are not used for anything,
at least in the usual workflow.
> In case of deprotonated the strecic slashes and repulsions would be more.
I'm not sure whether you had a chance to read my earlier post about
minimization of the deprotonated form:
> > >
> > > 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
Be sure the coordinates you are using here are the same ones you are using for
the checkValidity command. [I'm not really sure what checkValidity does, so
play safe and use the "checkoverlap" action in cpptraj: that will show you
your bad bond lengths (which you seem to have) and where the bad clashses
are.]
However, you might just be able to minimize the structure you have and
continue. As far as I remember, you only posted the first step for the
deprotonated form, but not what happens later on.
Short summary:
(1) for the protonated phosphates, you need to make force field modifications
along the lines of those in frcmod.phosaa10. [You'll have to do this by hand,
I think.]
(2) for the deprotonated forms, first just try some minimization.
....dac
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Received on Wed Aug 19 2015 - 08:00:05 PDT
