Thanks dac for the advice. I tried adding the missing atom types by typing this while tleap is running:
addAtomTypes {{ "C4D" "C" "sp2" }{ "ND" "N" "sp2" }{ "C1D" "C" "sp2" }{ "CAC" "C" "sp2" }{ "CBC" "C" "sp2" }{ "CBB" "C" "sp2" }{ "NB" "N" "sp2" }{ "CAB" "C" "sp2" }{ "C1B" "C" "sp2" }}
but I still get the same error messages. I also tried adding it to the addatomtypes section of the leaprc.ff99SB but still no success. What is my mistake?
Thanks
On 2012-10-31, at 10:55 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Oct 31, 2012, Maximilian Ebert wrote:
>
>> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
>> +---Tried to superimpose torsions for: *-C4D-ND-*
>> +--- With Sp2 - Sp0
>> +--- Sp0 probably means a new atom type is involved
>> +--- which needs to be added via addAtomTypes
>
> These are just warnings, but you might want to add missing atom types
> the in the addAtomTypes section of your leaprc file. Presumably, all the
> missing ones are from the heme library.
>
> ...good luck...dac
>
>
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Received on Wed Oct 31 2012 - 09:00:04 PDT
