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
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>>
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Received on Wed Feb 28 2018 - 05:30:03 PST
