[AMBER] descrepancy in net charge - TI output

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Mon, 30 Aug 2021 02:28:28 +0000

Dear amber users and developers,

I have attempted a thermodynamic integration for absolute binding free energy estimation. I noticed a difference in the net charge according to the ParmEd output and the TI mdout for TI region 1. I have utilized the same topology file for the simulation and ParmEd both. In theory, I believe those should be the same for my TI mask for region 1. I appreciate a clarification in this regard.

TI mdout

 begin time read from input coords =216149.999 ps

 Number of triangulated 3-point waters found: 13886

     Sum of charges for TI region 1 = 26.00000000
     Assuming uniform neutralizing plasma

     Sum of charges for TI region 2 = 22.00000000
     Assuming uniform neutralizing plasma

ParmEd output

Reading input from STDIN...
> parm complex_solv.prmtop
Adding prmtop complex_solv.prmtop to parm list. complex_solv.prmtop is the active parm.
> netCharge
The net charge of :* is 8.0000

Thank you

Senal Liyanage
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Received on Sun Aug 29 2021 - 19:30:02 PDT
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