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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 28 2018 - 05:00:02 PST
