Hi Ruth,
Just to follow up, did you remove the white space between addAtom Types to
make it addAtomTypes?
Regards,
Kellon
On Wed, Feb 28, 2018 at 8:01 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Dear Karolina,
>
> Unfortunately, it’s not a typo. The white space is indeed there (don’t
> know why it didn’t appear when I copied/pasted the command). I’ve tried
> again, in case, and I still get the same error message..
> Thanks anyway!
>
> Ruth
>
>
> > On 28 Feb 2018, at 13:55, Karolina Mitusińska (Markowska) <
> markowska.kar.gmail.com> wrote:
> >
> > 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
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 28 2018 - 10:30:02 PST
