Dear Kellon,
Thank you for your message!
I indeed misunderstood the previous suggestion made by Karolina. I though she referred to a missing white space when she actually meant that there was an extra white space as you clarify it.
Without the white space it works!
Thanks again,
Ruth
> On 28 Feb 2018, at 18:59, Kellon Belfon <kellonbelfon.gmail.com> wrote:
>
> 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
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>>>>
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>>
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Received on Wed Feb 28 2018 - 11:30:02 PST
