Hi Anselm,
Glad it worked. FYI, if you want to generate a bunch of structures you
could also use a loop like:
# System definition
parm r_cg.top [rtop]
# Solvent definition in SIRAH
solvent :WT4 crdset
loadcrd r_cg_A.crd [rcrd] parm [rtop]
for i=0;i<10;i++
crdaction [rcrd] randomizeions :ClW
crdout [rcrd] random.$i.mol2
done
-Dan
On Tue, Jan 23, 2024 at 9:36 AM Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
> Hi Dan,
>
> great, it worked!
>
> I used the simplest way you suggested, i.e. putting the 'solvent'
> command after the 'parm' but before 'loadcrd', and omitted the first
> 'crdout'; then used the crdaction/crdout command pair several times to
> create a set of structures with different ion positions, but same top file.
>
> (Actually, I was not aware of a 'crdset' keyword for 'solvent', but
> neither did I know about the magic 'loadcrd' does with the topology.)
>
> Many thanks for your prompt help!
>
> Best regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
> Am 23.01.2024 um 15:16 schrieb Daniel Roe:
> > 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
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 23 2024 - 07:30:02 PST
