Enrico, please use the Amber mailing list (not the ChimeraX list) for discussions that focus on Amber issues - thanks!
Elaine


> On Apr 24, 2024, at 2:47 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> ops sorry I forgot that the library should be loaded not sourced, BUT apparently it did not work with phosparilated residues. While loading the example with two such residues it create two new hydrogens
>
> Loading library: /opt/site/ubuntu_22.04/amber/22b/dat/leap/lib/terminal_monophosphate.lib
> Loading PDB file: ./proc2_bu.pdb
> Created a new atom named: HO5' within residue: .R<DG5 733>
> Created a new atom named: HO5' within residue: .R<DG5 758>
>   total atoms in file: 13034
>   Leap added 4 missing atoms according to residue templates:
>        4 unknown element
>   The file contained 2 atoms not in residue templates
>
> but then
>
> FATAL:  Atom .R<DG5 733>.A<HO5' 36> does not have a type.
> FATAL:  Atom .R<DG5 758>.A<HO5' 36> does not have a type.
>
> In my tleap script I used in the following combination:
> source leaprc.protein.ff19SB
> source leaprc.water.tip3p
> source leaprc.DNA.OL15
> loadoff terminal_monophosphate.lib
>
> Il giorno mer 24 apr 2024 alle ore 11:40 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
> 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
> >