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
Received on Sun Oct 04 2015 - 15:00:04 PDT
