In the past, individually, I have had issues with both SKETCHER and PRODRG.
A work around that seemed to work for me was building the molecule in
PRODRG, loading it into SKETCHER and then saving it, using the library
file generated by Sketcher for refinement in REFMAC or whatever.
Elbow in PHENIX worked great for me too.
cheers
charlie
> Hi Rui, for some reasons, I also always encounter problems when building
> new
> ligand by CCP4 Sketcher. You can try PRODRUG (
> http://davapc1.bioch.dundee.ac.uk/prodrg/index.html) to build your new
> ligand and get the cif from the server, it always works for me.
>
> HTH,
> Matt
>
> 2009/11/27 rui <[log in to unmask]>
>
>> Hi,
>>
>> I found this old post in ccp4 and it's very useful. I used the same
>> procedure Scott described to add a ligand into pdb file. What I did, is
>> in
>> coot, search for the ligand in the library and find the ligand and then
>> merge. However, when I tried to refine in refmac, it has some problems,
>> it
>> complains about that "New ligand has been encountered, stop now". I
>> didn't
>> create the cif file myself, it's been pulled from the library directory.
>> Do
>> anyone know what could be wrong? Thanks a lot for your help.
>>
>> Thanks.
>>
>> On Thu, Feb 5, 2009 at 10:55 AM, Scott Pegan <[log in to unmask]> wrote:
>>
>>> Andy,
>>>
>>> We do a lot of liganding fitting with CCP4. This is the general order
>>> of
>>> steps we take (post initial solution of the protein itself):
>>>
>>> 1) Build the potential ligand in CCP4 Sketcher
>>>
>>> a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with
>>> Hydrogens marked OH1, NH1, etc. To simplify things I normally just
>>> renumber
>>> all the Hydrogens starting from 1. Also makes for less hassle when
>>> using
>>> the definition file, as the labels in the definition file has to match
>>> the
>>> pdb of the ligand (this will be more important below).
>>>
>>> b) Use the regularize function with Refmac
>>>
>>> 2) Using Coot, load the protein and maps
>>>
>>> 3) Load the ligand and definition file (####_mon_lib.cif)
>>>
>>> 4) Use the find ligand function in Coot (find it under other modeling
>>> tools)
>>>
>>> a) select the protein, map you want to search
>>>
>>> 5) If you find results you desire, merge those ligands with the main
>>> pdb
>>>
>>> 6) Run Refmac on the merged PDB with the library for the ligand in the
>>> library input space.
>>>
>>> Hope this helps,
>>>
>>> Scott
>>>
>>> On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS
>>> <[log in to unmask]>wrote:
>>>
>>>> Hello,
>>>>
>>>> does anyone know of a tutorial which lays out some sort of pipeline,
>>>> hopefully using CCP4 packages, to fit and refine a small molecule
>>>> ligand please?
>>>>
>>>> cheers
>>>>
>>>> andy
>>>>
>>>>
>>>
>>>
>>> --
>>> Scott D. Pegan, Ph.D.
>>> Senior Research Specialist
>>> Center for Pharmaceutical
>>> Biotechnology
>>> University of Illinois at Chicago
>>>
>>
>>
>
>
> --
> --------------------------------------------------------------------------------------------
> Matthew L.H. Chu, PhD
> The University of Manchester, UK
> Hong Kong Tel: (852) 26729515 [home] / (852) 9169 2427 [mobile]
> Email: [log in to unmask]
> Facebook: http://www.facebook.com/MatthewLingHonChu
> MSN: [log in to unmask]
> Skype: matthew.lh.chu
> --------------------------------------------------------------------------------------------
>
|