Hello,
I am trying to make a simple electrostatic analysis of a molecular
system, so I am applying pbsa using inp=0 and radiopt=0 (no NP term and
use the solvation radii as contained in the topology file).
pbsa complains about a missing radius:
SA Bomb in phi_aaradi(): No radius assigned for atom 7 2C
However, for atom 7 there is a GB radius set in the topology file:
$ echo 'printDetails .7' | parmed.py -n ../molecule.prmtop
Loaded Amber topology file ../molecule.prmtop
Reading input from STDIN...
>
The mask .7 matches 1 atoms:
ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass
Charge GB Radius GB Screen
7 1 SER CB 2C 1.9080 0.1094 12.0100
0.2596 1.7000 0.7200
> Done!
I used 'set default pbradii bondi' in leap when creating that topology
file. I am using AmberTools 13 with the latest patches for pbsa. The
whole pbsa input file is this:
&cntrl
inp=0,
/
&pb
npbopt=0,
radiopt=0,
npbverb=0,
space=1,
fillratio=1.0,
sasopt=2,
phiout=1,
phiform=2,
npbverb=1,
/
So, what is the issue here? Why is the given radius not used?
Thanks,
Jan-Philip
PS . Jason:
"parmed.py ../molecule.prmtop 'printDetails .7'" does not, which I did
not expect. In the help message the last argument is described as
"[<script>]". I read from this that <script> should be string containing
parmed commands. However, the latter is interpreted as path to a file.
But there is an additional option (-i FILE) for specifying a path to a
script file. So, are there currently two ways to specify a path to a
script file and no way to directly provide a command string?
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Received on Mon Nov 25 2013 - 10:00:02 PST
