Adding a dummy atom to the PQR file without interfering the calculation

[rwxayheee]

Dear APBS experts,

I'm using APBS version 3.2.1 on Linux x86_64 OS, and I was using the "mg-auto" mode to calculate the electrostatic potential map of a protein.

And I need to add a dummy atom (with no radius and no charge) to the PQR file. The dummy atom is added at the end of the PQR file:

(protein atoms)
ATOM 8259 OXT THR 543 63.532 103.325 -14.812 -0.8044 1.6612
ATOM 8260 HG1 THR 543 67.879 103.234 -16.564 0.4119 0.0000
TER
ATOM 9999 UNK FOO 999 91.488 86.764 -3.189 0.0 0.0
END

From the standard output of APBS calculation, I checked the "Total electrostatic energy" value at the last step "CALCULATION #3: MULTIGRID" for the fine mesh region. There seems to be a minor difference (~0.5 kJ/mol) caused by adding the dummy atom: same calculation without the dummy atom gives a total electrostatic energy of 2.384663622213E+05 kJ/mol, and the calculation with the dummy atom gives a total electrostatic energy of 2.384669050542E+05 kJ/mo.

Could you please tell me what is the correct syntax to completely exclude the dummy atom from the calculation?

Thank you for your kind advice in advance.

Bests,
Amy

[sobolevnrm]

Hello -- what dielectric surface definition (srfm) are you using?

[rwxayheee]

Hi Nathan, Thank you for your kind reply. I'm using "smol". My input file is as follows:

read
mol pqr protein.pqr
end
elec
mg-auto
dime 289 289 289

cglen 1000 1000 1000
fglen 144 144 144

cgcent mol 1
fgcent mol 1

mol 1
lpbe
bcfl sdh

ion 1 0.1 1.62 # Na+ Born radius, doi/10.1021/jp509445k
ion -1 0.1 2.26 # Cl- Born radius, doi/10.1021/jp509445k

pdie 4
sdie 78
srfm smol

chgm spl2

sdens 10.0
srad 1.40
swin 0.30
temp 298
calcenergy total

calcforce no
write pot dx protein

end
quit

[sobolevnrm]

Hello --

srfm mol and srfm smol will generate surface contributions from zero-radius atoms. They probably shouldn't do that but that's a low-priority bug to fix.

What are you trying to accomplish with the dummy atom? There may be other ways to get the information you're looking for.

Thank you

[rwxayheee]

Hi Nathan,
Thank you for your kind reply. I'm doing Brownian Dynamics simulations in program Browndye, and I was trying to define the reaction surface by a sphere centered at the geometric center of a few atoms. Since the dummy atom might be taken into account in APBS calculation, I will try to defined the surface by a combination of actual atoms instead. Thank you again for the information!

Thanks,
Amy