Dear Amber-community,
I performed crystal simulations of rnaseA (one unit cell consists of 6
copies of the asymmetric unit). For further analysis I need to align the
unit cells of each snapshot. For that I am using the xtalsymm function
of cpptraj, but I always get a segmentation fault.
Would you like to help me please?
Below you will find additional information, which might be helpful.
CRYST1 64.700 64.700 65.200 90.00 90.00 120.00 P 32 2 1
CPPTRAJ: Trajectory Analysis. V5.1.0
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 01/11/23 15:27:10
| Available memory: 6.463 GB
> parm rnasea_unitcell4025.prmtop
[parm rnasea_unitcell4025.prmtop]
Reading 'rnasea_unitcell4025.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
> trajin rnasea_unitcell4025.inpcrd
[trajin rnasea_unitcell4025.inpcrd]
Reading 'rnasea_unitcell4025.inpcrd' as Amber Restart
Warning: Trajectory box type is 'Hexagonal' but topology box type is
'Tetragonal'.
Warning: Setting topology box information from trajectory.
> trajin production.nc
[trajin production.nc]
Reading 'production.nc' as Amber NetCDF
> xtalsymm :1-124,128-251,255-378,382-505,509-632,636-759 group
'P3(2)21' collect centroid first
[xtalsymm :1-124,128-251,255-378,382-505,509-632,636-759 group
'P3(2)21' collect centroid first]
XTALSYMM: Mask is :1-124,128-251,255-378,382-505,509-632,636-759
Reference is first frame.
Space group 'P3(2)21'
NA= 1 NB= 1 NC= 1 Nops= 6
Reimaging by molecule
> run
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: rnasea_unitcell4025.prmtop, 29624 atoms, 5393 res, box: Hexagonal,
4655 mol, 4607 solvent
INPUT TRAJECTORIES (2 total):
0: 'rnasea_unitcell4025.inpcrd' is an AMBER restart file, no
velocities, Parm rnasea_unitcell4025.prmtop (Hexagonal box) (reading 1 of 1)
1: 'production.nc' is a NetCDF AMBER trajectory with coordinates,
time, box, Parm rnasea_unitcell4025.prmtop (Hexagonal box) (reading 25
of 25)
Coordinate processing will occur on 26 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'rnasea_unitcell4025.prmtop' (1 actions):
0: [xtalsymm :1-124,128-251,255-378,382-505,509-632,636-759 group
'P3(2)21' collect centroid first]
----- rnasea_unitcell4025.inpcrd (1-1, 1) -----
j = 0 out of 0 atoms, i = 0 out of 1 capacity.
Segmentation fault (core dumped)
By using "parmbox x 64.7 y 64.7 z 65.2 alpha 90 beta 90 gamma 120" I
could disable the warnings, but the seg fault remained.
Thanks in advance,
Thorben
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Received on Wed Jan 11 2023 - 08:00:03 PST
