As one simple thing to try, I would add/assume a residue already in
place to be mutated, and edit a copy of the pdb file to change the
residue name and names of atoms that can be used in the new residue,
then loadpdb and see how bad the coordinates of added atoms look.
Bill
On 9/13/18 12:15 AM, Benjamin Clausen wrote:
> Would you mind sharing how you would go about using leap to build a side chain?
>
> ________________________________
> Fra: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sendt: 12. september 2018 18:25:16
> Til: AMBER Mailing List
> Emne: Re: [AMBER] Residue mutation and side chains
>
> Leap can build them, but it doesn't have a good way to optimize their
> rotamers prior to MD.
> I suggest using tools made for this purpose, like those in swissPDBviewer,
> or the SCWRL program. There are probably others too, and it depends on
> whether your mutations are solvent exposed (fairly easy) or buried (harder).
>
>
> On Wed, Sep 12, 2018 at 7:02 AM Benjamin Clausen <s153989.student.dtu.dk>
> wrote:
>
>> Hello
>>
>>
>> I am trying to carry out a residue mutation in AMBER. As far as I have
>> understood I can use "pdb4amber" to mutate residues, but the resulting
>> mutations only leave the backbone in the pdb file. Is there any way I can
>> make AMBER put in the missing side chain of the mutated residues?
>>
>> The input I have used for mutation is:
>> pdb4amber -i in.pdb -o out.pdb -m "94-GLY,94-ASP,217-GLU,217-GLN"
>>
>>
>> Best regards Benjamin
>>
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>>
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Received on Thu Sep 13 2018 - 00:30:03 PDT
