Dear Ruth,
for me it look like you have a typo, an additional white space in the
command between Atom and Types.
addAtomTypes{
vs
addAtom Types{
Have a nice day!
Karolina Mitusińska
PhD student
2018-02-28 13:46 GMT+01:00 Ruth Helena Tichauer <rhtichau.laas.fr>:
> Dear Amber users/developers,
>
> Few days before, I’encountered the following problem when building
> parameter and coordinate files with tleap, reported in the leap.log file
> only:
>
> > source oldff/leaprc.ff99bsc0
> > loadoff mga.lib
> Loading library: ./mga.lib
> Loading: MGA
> > loadamberprep gtp.prep
> Loading Prep file: ./gtp.prep
> (UNKNOWN ATOM TYPE: O3)
> (UNKNOWN ATOM TYPE: O3)
> (UNKNOWN ATOM TYPE: O3)
> Loaded UNIT: GTP
> > loadamberparams gtp.frcmod
> Loading parameters: ./gtp.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> # Modifications to the AMBER94 force field for polyphosphates
> (UNKNOWN ATOM TYPE: O3)
>
> Professor David Case, gave me the following workaround:
>
> addAtomTypes{
> { "O3" "O" "sp2" }
> }
>
> But now that I try to apply it again (as I still get the same "UNKNOWN
> ATOM TYPE: O3" error message), it does not work any more:
>
> Welcome to LEaP!
> (no leaprc in search path)
> > addAtom Types{
> > {"O3" "O" "sp2"}
> > }
> ERROR: syntax error
>
> Any idea on how to solve this? My Ambertools version is:
>
> ./update_amber --version
> Version is reported as <version>.<patches applied>
>
> AmberTools version 16.22
> Amber version 16.12
>
> Thank you for any insight in solving this problem,
>
> Sincerely,
>
> Ruth
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Received on Wed Feb 28 2018 - 05:00:04 PST
