Dear David,
I’ve managed to check the version it is
./update_amber -v
Version is reported as <version>.<patches applied>
AmberTools version 16.21
Amber version 16.07
Thank you again for any help,
Ruth
> On 12 Feb 2018, at 14:57, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> Dear David,
>
> Thank you for having a look into this problem.
> I’m using Ambertools V16.16 (I looked into cpptraj as I didn’t know how else to get the version.. It must be anyway the version that was released for Amber 16).
>
> I’ve tried adding:
>> addAtomTypes{
>> { "O3" "O" "sp2" }
>> }
> just after sourcing the forcefield in leap (exactly like this) but it didn’t change anything.. I still get an “UNKNOWN ATOM TYPE” message in the leap.log file although no error message arises during the run and the parameters and coordinates files are created.
>
> Here are just in case the .prep and .frcmod files.
> Thank you for helping me solve this problem,
>
> Sincerely,
>
> Ruth
>
> <gtp.frcmod><gtp.prep>
>
>
>
>> On 12 Feb 2018, at 13:44, David A Case <david.case.rutgers.edu> wrote:
>>
>> On Fri, Feb 09, 2018, Ruth Helena Tichauer wrote:
>>>
>>> When trying QM/MM with an internal QM method, it appears that the atom type of three oxygens from my ligand are unknown. Here is the error message:
>>>
>>> QMMM: Atom number: 107 has atomic number -1
>>>
>>>> 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)
>>
>> I'm unable to reproduce these "UNKNOWN ATOM TYPE" messages. What version of
>> AmberTools are you using?
>>
>> Try loading the following in leap, at the beginning:
>>
>> addAtomTypes{
>> { "O3" "O" "sp2" }
>> }
>>
>> That should force leap to recognize that atom type O3 is in oxygen.
>>
>> ...hope this helps....dac
>>
>>
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>
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Received on Mon Feb 12 2018 - 06:30:05 PST
