How many residues? If there are more than a few, you may want to find a
structure (e.g. from Brookhaven PDB) for a similar sequence and adapt
it. If it's something that wouldn't have stable folding, starting
structure is less important.
Bill
On 4/4/16 6:25 PM, YanhuaOuyang wrote:
> In fact, I just have a fasta file of the protein sequence, I just don’t know how to convert the peptide sequence to a pdb file of a protein which is phosphorylated at Serine and Threonine. Can you tell me the detailed steps.
>>>> and Threonine
>> 在 2016年4月5日，上午9:04，YanhuaOuyang <15901283893.163.com> 写道：
>>
>> I have the pdb file just has Ser and Thr I want to change them to make them
>> phosphorylated.
>>> 在 2016年4月4日，下午6:10，Carlos Simmerling <carlos.simmerling.gmail.com> 写道：
>>>
>>> It's not clear what you are trying to do. Are you saying that the pdb file
>>> just has Ser and Thr and you want to change them to make them
>>> phosphorylated? Or are you asking how to get parameters?
>>> On Apr 4, 2016 3:21 AM, "YanhuaOuyang" <15901283893.163.com> wrote:
>>>
>>>> Hi, I am preparing pdb file of a protein which is phosphorylated at Serine
>>>> and Threonine. I first do a phosphorylated protein, so I don’t know how to
>>>> build my phosphorylated protein structure pdb file. Is it build using
>>>> softwares, then which one? What the detailed steps of building such a pdb
>>>> file? How to add a phosphate group in the pdb file?
>>>>
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Received on Mon Apr 04 2016 - 19:00:02 PDT
