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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