Hi Anselm,
Thanks for the files. After looking at your input again however I saw
something I missed initially. The 'loadcrd' command essentially
creates a separate copy of whatever topology you are using (i.e. the
data set is self-contained, unlike when you use 'trajin'). You're
using the 'solvent' command after 'loadcrd', so it is affecting the
first loaded topology, not the one in your COORDS data set [rcrd]. You
need to either put the 'solvent' command before 'loadcrd' (so it
affects the loaded topology) or use the 'crdset' keyword in the
solvent command to make sure the COORDS set topology is modified.
Also, since you're using a COORDS data set and not 'trajin', you don't
need 'go'. However, you probably want to write the resulting
trajectory, so use 'crdout'. Here's your input slightly modified:
# System definition
parm r_cg.top [rtop]
loadcrd r_cg_A.crd [rcrd] parm [rtop]
crdout [rcrd] initial.mol2
# Solvent definition in SIRAH
solvent :WT4 crdset [rcrd]
crdaction [rcrd] randomizeions :ClW
crdout [rcrd] random.mol2
Let me know if that works for you.
-Dan
On Tue, Jan 23, 2024 at 8:28 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi Anselm,
>
> Can you send me the top/crd (1 frame will do) off-list? Thanks.
>
> -Dan
>
> On Tue, Jan 23, 2024 at 5:40 AM Dr. Anselm Horn via AMBER <amber.ambermd.org> wrote:
>>
>> 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 - 06:30:01 PST
