[phenixbb] Duration of a phenix.elbow run

chern chern at ualberta.ca
Thu Jul 2 08:01:34 PDT 2009


Hi Carsten,
is there a simple program  for a MM minimization of the ligand? The prodrg 
server changes atom labels and therefore is not convenient. Do you use sybyl 
or what else?

Maia

----- Original Message ----- 
From: "Schubert, Carsten [PRDUS]" <CSCHUBER at its.jnj.com>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Thursday, July 02, 2009 7:49 AM
Subject: Re: [phenixbb] Duration of a phenix.elbow run


> What I do in these cases is a MM minimization of the ligand using a high
> quality forcefield and using that output as input into elbow and not
> perform an optimization, but have it generate the restraints directly
> from the input. The differences between the forcefield and the AM1
> calculation in elbow are negligible for protein crystallography
> purposes. I would not waste time on o.n. runs.
>
> HTH
>
> Carsten
>
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
>> bounces at phenix-online.org] On Behalf Of Nigel W Moriarty
>> Sent: Wednesday, July 01, 2009 7:26 PM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] Duration of a phenix.elbow run
>>
>> Dirk
>>
>> That is quite a large molecule but it shouldn't take a few hours.  I'm
>> not sure what is happening but I'd guess that a convergence is failing
>> and the upper limit on the number of steps is too great.  If I was
> you,
>> I'd run it overnight and if that fails run it in another quantum
>> package
>> to get the geometry you desire.  A different run MAY generate a
>> different starting geometry for the --opt option and that may work
>> better.  Each step of the optimisation should take less than 2
> minutes.
>>
>> Nigel
>>
>> On 7/1/09 2:43 PM, Dirk wrote:
>> > Hi,
>> >
>> > I'm trying to create restraints for a carbohydrate ligand using
>> > phenix.elbow. If I run it without the --opt command everything works
>> > fine, but I'm not completely happy with the geometry of my ligand
>> after
>> > refinement. I tried to get an optimized cif by using --opt command,
>> but
>> > the program just runs up to the following output:
>> >
>> > MoleculeClass :  H:38  C:23  N: 1  O:19 (PDB format)
>> >         81 atoms
>> >         83 bonds
>> >         151 angles
>> >         238 dihedrals
>> >         --------------------
>> > Time      Energy        delta E    RMS         Max      Step size
>> >
>> >
>> > and then nothing happens for several hours. Does the optimization
>> needs
>> > such a long time and if I let it run overnight (or perhaps longer) I
>> > will get an output or is something going wrong?
>> > The input is a pdb (I tested several) and I tried both the stable
>> phenix
>> > release (1.3) and the current version (1.4).
>> >
>> > Any help would be very appreciated
>> >
>> > Thanks
>> >
>> > Dirk
>> >
>> > _______________________________________________
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>> > phenixbb at phenix-online.org
>> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>> >
>> >
>>
>> --
>> Nigel W. Moriarty
>> Building 64R0246B, Physical Biosciences Division
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709
>> Fax   : 510-486-5909
>> Email : NWMoriarty at LBL.gov
>> Web   : CCI.LBL.gov
>>
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>
>
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