Dear Jason,
Could you please explain these terminologies in .cpin file from your explicit solvent CpHMD wikidot page and few other questions.
STATEINF(0)%FIRST_CHARGE ? Is this total charge of the first residue ? I see 0, 95, 149 etc. in the list which didn’t make sense to me.
STATEINF(0)%FIRST_STATE ? I see 0, 5 , 8 as values. Initially I thought its different states of a residue. But “8” ?
STATENE=0,21.2486237123,21.2486237123,21.2486237123,21.2486237123…..what are these values ? Also why is first value zero ?
I calculated reference energies values for my model organic compound (CH3)3-C-COOH both in explicit and implicit solvent. Explicit solvation (IGB=0), I got -62.3070 kcal/mol (anti-) and -61.2687 kcal/mol (-syn). In Implicit solvation with O-radii = 1.5, I got -51.5209 kcal/mol (-anti) and -50.5030 kcal/mol (-syn) while changing O-radii to 1.3 gave me -59.8513 kcal/mol (-anti) and -59.0642 (-syn). As you see values are not close for explicit solvation and implicit solvation (1.5 radii) and slightly closer with smaller radii (1.3). Does it makes sense, even though values of explicit and implicit (1.3 radii) don’t match ?
Also as you can see -anti is slightly favored over -syn. I’m not sure which one do I use as IGB2 value ? is it possible to use two values ?
In AMBER manual you specify that reference energy value calculated using TI is assigned to the unprotonated form and reference energy value to the protonated form is increased by adding pKaRTln(10) to that value. I’m not clear on this assigning part. Isn’t the reference energy the difference between two states ? are reference energy and relative energy one and the same ?
I ran explicit solvent CpHMD (same parameters as in TI calculations) at pH=pKa but I don’t see 50% protonation. It’s stuck at the starting residue state and there is no transition. I guess reference energy value is not right. But I don’t see anything wrong with the reference energy value calculated using sander TI method.
I would really appreciate your help.
Thanks
A
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Received on Tue Oct 06 2015 - 07:30:03 PDT
