Hi, thanks for the suggestions I tried to run it overnight, but without any result. I also tried to use GAMESS, but even so the GAMESS run is started I still get the message "GAMESS doesn't seem to be installed" and "mv: Aufruf von stat für „elbow.drgfin_pdb.012.gamess.gam“ nicht möglich: No such file or directory" even so the file exists. Since I'm not experienced in python I wasn't able to find the reason for that by inspecting the GAMESSMixins.py script. I would like to try the forcefield approach, but don't know if there is any freeware available for that purpose - I would be glad about suggestions . For the moment I "solved" the problem by manually editing the cif file using values from the refmac monomer and link libraries for the restraints. I still would be really interested in getting elbow to work to get better restraints for this ligand and to avoid the time consuming manual creation of cif files in the future. Thank you again for the replies Dirk Schubert, Carsten [PRDUS] schrieb: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: [email protected] [mailto:phenixbb- [email protected]] 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 wasyou,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 2minutes.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 ligandafterrefinement. I tried to get an optimized cif by using --opt command,butthe 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 optimizationneedssuch 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 stablephenixrelease (1.3) and the current version (1.4). Any help would be very appreciated Thanks Dirk _______________________________________________ phenixbb mailing list [email protected] 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 : [email protected] Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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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 : [email protected]
Web : CCI.LBL.gov