If I only load the Ser-PPP by itself (or both independently) the valence
isnt met without adding extra hydrogens...
On Wed, Jun 29, 2011 at 2:36 PM, David Cantu <cantudav.gmail.com> wrote:
> Hi Ben,
>
> Do I use reduce and antechamber with the entire PDB? How do I choose only
> the 1 residue (combined Ser-PPP) for antechamber?
>
> David
>
>
> On Wed, Jun 29, 2011 at 12:50 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
>
>> Hi David,
>>
>> On 29/6/2011, at 1:38 p.m., David Cantu wrote:
>>
>> > Dear Amber Users/Developers,
>> >
>> > We have a protein, which has a phosphopantethiene group (call it resiude
>> > PPP) attached to a serine (through a P-O bond). We tried loading this
>> > Ser-PPP residue into antechamber, but failed.
>> >
>> > If we load the PPP by itself, using Antechamber, a hydrogen will take
>> the
>> > place of the P-O bond. We cannot load it with an open valence. Any ideas
>> no
>> > how to load both the PPP and Ser as a non-standard resiude? We need the
>> > correct parameters for the P-O bond.
>>
>> About the only thing I can suggest is to combine the PPP and serine into a
>> single residue, with its own three-letter residue code and residue number.
>> Then,
>> antechamber should handle it without any problems.
>>
>> Good luck!
>>
>> Ben
>>
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Received on Wed Jun 29 2011 - 15:30:03 PDT
