Thank you very much David !

Actually I've tried to source this lib but,

> source leaprc.DNA.OL15
----- Source: /opt/site/ubuntu_22.04/amber/22b/dat/leap/cmd/leaprc.DNA.OL15
----- Source of /opt/site/ubuntu_22.04/amber/22b/dat/leap/cmd/leaprc.DNA.OL15 done
Log file: ./leap.log
Loading library: /opt/site/ubuntu_22.04/amber/22b/dat/leap/lib/DNA.OL15.lib
Loading parameters: /opt/site/ubuntu_22.04/amber/22b/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /opt/site/ubuntu_22.04/amber/22b/dat/leap/parm/frcmod.DNA.OL15
Reading force field modification type file (frcmod)
Reading title:
OL15 force field for DNA (99bsc0-betaOL1-eps-zetaOL1-chiOL4) see http://ffol.upol.cz
> source the terminal_monophosphate.lib

Error: source: Improper number of arguments!
usage:  source <filename>
> source terminal_monophosphate.lib    
----- Source: /opt/site/ubuntu_22.04/amber/22b/dat/leap/lib/terminal_monophosphate.lib
----- Source of /opt/site/ubuntu_22.04/amber/22b/dat/leap/lib/terminal_monophosphate.lib done

/opt/site/ubuntu_22.04/amber/22b/bin/teLeap: Fatal Error!
Error from the parser:
       syntax error.
       Check for typos, misspellings, etc.
       Try help on the command name and desc on the command arguments.

Exiting LEaP: Errors = 2; Warnings = 0; Notes = 0.

Il giorno mar 23 apr 2024 alle ore 23:36 Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> ha scritto:
Sorry I got that wrong, and good to know!

--Eric

> On Apr 23, 2024, at 2:34 PM, David A Case via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> On Tue, Apr 23, 2024, Eric Pettersen via ChimeraX-users wrote:
>
>> I wouldn't call having the 5' end of a nucleic acid chain phosphorylated a
>> problem.  Some entries have that (e.g. 6zz6) and some don't (e.g. 1bna).
>> Amber doesn't support 5' phosphorylation simulation, so as you found you
>> need to delete it yourself.
>
> FWIW: Amber *does* support 5' phosphorylation, but it is admittedly not
> well-described in the documentation (should change soon.)  You need to
> load the "terminal_monophosphate.lib" file after loading the standard DNA or
> RNA leaprc files.
>
> [Things are more complicated if you need to control the protonation states,
> or if some chains have a 5' phosphate and others do no, etc.]  Don't
> hesitate to ask questions at the Amber mailing list.]
>
> ...dave case
>
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