Okay I read that for the preparation of the topology file I can ignore these error messages. However, if someone knows why the addAtomTypes command does not work in my case I would be happy to hear about it.
Another question I have is regarding the CONECT section in the PDB. Is it really a good idea to delete these for the preparation? I read in a tutorial that this should be done. But in the case of P450 cytochromes it defines the heme ligand and the binding with the protein through a cysteine. Wouldn't this affect my simulation if all the information is gone?
Thank you very much!
Max
On 2012-10-31, at 11:53 AM, Maximilian Ebert <m.ebert.umontreal.ca> wrote:
> 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 Thu Nov 01 2012 - 08:30:03 PDT
