Dear Wei,
Great! I am now able to avoid sleap segfault and "saveamberparm" units
with non-solvated water.
Here are some test results:
----------
% env AMBERHOME=~/amber11 ~/amber11/bin/sleap
[gtkleap]$ source leaprc.ff99SB
[gtkleap]$ mymol = sequence {WAT}
Sequence: WAT
[gtkleap]$ saveamberparm mymol 1.prmtop 1.inpcrd
[gtkleap]$ mymol = loadpdb TP3.pdb
[gtkleap]$ saveamberparm mymol 2.prmtop 2.inpcrd
[gtkleap]$ mymol = sequence {TP3}
Sequence: TP3
[gtkleap]$ saveamberparm mymol 3.prmtop 3.inpcrd
[gtkleap]$ saveamberparm TP3 4.prmtop 4.inpcrd
[gtkleap]$ saveamberparm WAT 5.prmtop 5.inpcrd
Error: molecule WAT doesn't exist.
[gtkleap]$ quit
% grep 1.5000000 ?.prmtop
1.prmtop: 1.50000000e+00 8.00000000e-01 8.00000000e-01
2.prmtop: 1.50000000e+00 8.00000000e-01 8.00000000e-01
3.prmtop: 1.50000000e+00 8.00000000e-01 8.00000000e-01
4.prmtop: 1.50000000e+00 8.00000000e-01 1.20000000e+00
----------
I am not sure if it's supposed to have a WAT unit, but apparently I
was able to use WAT as a sequence... :-) On the other hand, only
saving TP3 directly gives you 1.2 Å for the second HW radii.
I hope this helps furture debugging, so far I am quite happy to see
sleap running without segfault.
Thanks,
--
Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
University of California Irvine.
On Wed, Dec 02, 2009 at 09:54:25AM -0600, Wei Zhang wrote:
> Hi MengJuei,
> I fixed this bug and checked into CVS. Would you please try it again?
> Sincerely,
> Wei
> On Nov 30, 2009, at 4:46 AM, MengJuei Hsieh wrote:
> > mymol = loadpdb water.pdb
> > saveamberparm mymol water.prmtop water.inprst
> > sleap dies with segfault.
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Received on Thu Dec 03 2009 - 00:00:02 PST
