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
> 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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Received on Mon Feb 12 2018 - 06:00:05 PST
