Dear Amber experts,
I set up a solvated protein system using the SIRAH coarse grained force
field and now try to randomize the ions positions via the randomizeions
feature in cpptraj.
Unfortunately, my approach, which worked for atomistic topologies, does
not work here: cpptraj complains about a lacking definition of the
solvent, although it first seems to recognize it.
Is there an error in my input file or does randomizeions only work for
atomistic water models?
The cpptraj input is:
# System definition
parm r_cg.top [rtop]
loadcrd r_cg_A.crd [rcrd] parm [rtop]
# Solvent definition in SIRAH
solvent :WT4
crdaction [rcrd] randomizeions :ClW
go
The cpptraj output is:
CPPTRAJ: Trajectory Analysis. V6.18.1 (AmberTools)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 01/23/24 11:02:32
| Available memory: 4.489 GB
INPUT: Reading input from 'r_cg_randomizeions.cpptraj'
[parm r_cg.top [rtop]]
Reading 'r_cg.top' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
[loadcrd r_cg_A.crd [rcrd] parm [rtop]]
Reading 'r_cg_A.crd' as Amber Restart
Loading trajectory 'r_cg_A.crd' as '[rcrd]'
----- r_cg_A.crd (1-1, 1) -----
[solvent :WT4]
Mask [:WT4] corresponds to 45896 atoms.
Solvent Mask [:WT4]: 11474 solvent molecules, 45896 solvent atoms
[crdaction [rcrd] randomizeions :ClW]
Using set '[rcrd]'
----- [rcrd] (1-1, 1) -----
RANDOMIZEIONS: Swapping postions of ions in mask ':ClW' with solvent.
No ion can get closer than 3.50 angstroms to another ion.
RNG: Marsaglia
Random_Number: seed is <= 0, using wallclock time as seed ( 173917 )
Error: This command only works if solvent information has been specified.
1 errors encountered reading input.
TIME: Total execution time: 0.1601 seconds.
Error: Error(s) occurred during execution.
Helpful suggestions are appreciated!
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
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Received on Tue Jan 23 2024 - 03:00:02 PST
