I used gaussian to generate these charges and antechamber to generate
charges using resp charge method
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
On Sun, Oct 4, 2015 at 7:34 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
> at do you mean by "
>
> I assigned the charges using the AMBER 99SB FF"
>
> There is no succinic acid in FF99SB.
>
> adrian
>
> On 10/4/15 5:42 PM, Rahul Ramesh wrote:
> > Hello Jason
> > I'm trying to simulate a cellulosic molecule with a succinic group. (
> This
> > is my model compound as I am going to simulate a larger system in future
> )
> > I assigned the charges using the AMBER 99SB FF. I performed Thermodynamic
> > Integration of this structure and obtained a value of -25 kcal/mol.
> Since I
> > wanted to confirm the value of this del G ref against the pKa , I
> performed
> > a CpHMD at pH = pKa. I expected the system to be protonated/ deprotonated
> > 50 % of the time. But I end up getting 100% protonation. I used the same
> > set of parameters for both TI and CpHMD.
> > I went through the mdout file and the EEL , EGB and 1-4 EEL are not
> > convincing.
> >
> > NSTEP = 125000 TIME(PS) = 2250.000 TEMP(K) = 237.22 PRESS =
> > 0.0
> >
> > Etot = -262.6830 EKtot = 24.2773 *EPtot =
> > -286.9603*
> >
> > BOND = 21.5394 ANGLE = 26.4520 DIHED =
> > 24.9527
> >
> > 1-4 NB = 6.7956 *1-4 EEL = -89.1130* VDWAALS =
> > -3.9488
> >
> > *EELEC = -25.1198 EGB = -248.5186* RESTRAINT =
> > 0.0000
> >
> > The electrostatic energy is positive if you subtract 1-4 EEL from EELEC.
> > I'm thinking of a reason as to why the electrostatic energy is really low
> > and 1-4 EEL and EGB is really high?
> >
> > I compared my system (cellulosic molecule attached to a succinic group)
> to
> > a succinic acid (COOHCH2CH2COOH) system. Basically I simulated just the
> > side group of the cellulosic molecule using the AMBER99SB FF. I followed
> > the same procedure as above and I was able to get 50 % protonation at pH
> =
> > pKa and a del G ref as -22 kcal/mol ( pH = 4.2).
> >
> > I tried comparing the mdout file for succinic acid to the above mdout
> file
> >
> > *Protonated State for Succinic Acid*
> >
> > NSTEP = 999600 TIME(PS) = 3999.200 TEMP(K) = 545.62 PRESS =
> > 0.0
> >
> > Etot = -63.8361 EKtot = 19.5165 *EPtot =
> > -83.3526*
> >
> > BOND = 2.1652 ANGLE = 8.1213 DIHED =
> > 7.6514
> >
> > 1-4 NB = 0.8964 *1-4 EEL = 19.4734* VDWAALS =
> > -0.8920
> >
> > *EELEC = -93.5325 EGB = -27.2358* RESTRAINT =
> > 0.0000
> > *Deprotonated State for Succinic Acid*
> >
> > NSTEP = 999550 TIME(PS) = 3999.100 TEMP(K) = 438.95 PRESS =
> > 0.0
> >
> > Etot = -88.1985 EKtot = 15.7011 * EPtot =
> > -103.8997*
> >
> > BOND = 2.2672 ANGLE = 10.6449 DIHED =
> > 8.7225
> >
> > 1-4 NB = 0.6721 *1-4 EEL = 21.5060 * VDWAALS =
> > -1.0602
> >
> > *EELEC = -55.1840 EGB = -91.4680 *RESTRAINT =
> > 0.0000
> > For the Succinic Acid case , EELEC is negative and different between the
> > EPtot of the protonated and deprotonated is approximately the Del G ref.
> I
> > was expecting the same behavior for my cellulosic molecule attached to
> > succinic group.
> > Could you comment on the reason for EELEC being positive in the first
> case
> > and high value of 1-4 EEL and EGB
> >
> > Thank You
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Sun Oct 04 2015 - 18:00:03 PDT
