Re: [apbs-users] Solvent accessibility

[Baker, N. <nat...@pn...>]

Hello --

Can you please provide an example PQR file so we can attempt to reproduce the problem?

Thank you,



--

Nathan Baker
http://pronoun.is/he

Physical and Computational Sciences Directorate — Pacific Northwest Natl Lab
Department of Applied Mathematics — University of Washington
https://www.linkedin.com/in/nathanandrewbaker/

________________________________
From: Amaury Coste <ama...@ki...>
Sent: Monday, July 20, 2020 07:10
To: apb...@li... <apb...@li...>
Subject: [apbs-users] Solvent accessibility


Hello,


I am calculating density profiles of mobile ions and I highlight an issue. The ion accessibility is not set to 0 within the DNA put below the parameters and the output of the solvent accessibility around DNA molecule. Is it something wrong in my parameters or is it a problem of the code.

Thank you very much for your help.

Best regards,


Dr. Amaury Coste



read

mol pqr dna.pqr

end

elec name polar

mg-auto

dime 97 97 161

cglen 160 160 34

fglen 130 130 34

cgcent mol 1

fgcent mol 1

mol 1

lpbe

bcfl zero

pdie 1.0 #2

sdie 78.54 #75.5

ion charge 1.0 conc 0.15 radius 2 #

ion charge -1.0 conc 0.15 radius 2

srfm mol

chgm spl2

sdens 10.00

gamma 0.105

srad 0

swin 0.30

temp 298.15

calcenergy total #calculated apolar energy

calcforce no

write pot dx pot

write qdens dx qdens

write ndens dx ndens

write vdw flat vdw

end

quit





# Data from 1.4

#

# SOLVENT ACCESSIBILITY -- VAN DER WAALS

#

1.000000e+00

1.000000e+00

1.000000e+00

1.000000e+00

etc...