[phenixbb] phenix.elbow with Gamess, no cif restraint file

[Dyda]

Hi All,

I'm clearly doing something wrong, but don't know what. 

Trying to run elbow with Gamess from the command line for
"myligand" but no .cif file is produced. The input is a
pdb file of the ligand, this the best I have.   

The command line:

phenix.elbow --all-residues --do-all --gamess --basis=3D"3-21G" myligand.pdb > elbow.out &

Everything seems to be OK, Gamess is found and run:

> more elbow.out 

 ------------------------------------------------------------------------------
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.10.1-2155 None
    - Nigel W. Moriarty (NWMoriarty at LBL.Gov)
 ------------------------------------------------------------------------------

 Random number seed:  3628800
 Initial processing time : 0.01 seconds
 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P

Input format is PDB

MoleculeClass :  C:15  O: 6 Cr: 1 (PDB format)
        22 atoms
        0 bonds
        0 angles
        0 dihedrals
        0 rings
        0 chirals
 Predicted memory usage by semi-empirical method : 41Mb
 Timing estimates
     Python portion         / ATP : 62%
     c++ optimisation cycle / ATP : 47%
        Hydrogens may be required to determine the correct bonding

   Residue has metal at the centre of a coordination sphere. Using input
   geometry to generate restraints. Hydrogens may not be added.
   
 0:10 Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise Hydrogenise H
 1:49 ReCentre molecule for optimisation ReCentre molecule for optimisation ReC

        Optimisation software : GAMESS
        Quantum method        : UHF
        Quantum basis set     : 3-21G


        Opt steps       :  60
        Opt macro steps :   3
       
 Searching for flowchart file: flowchart.py
   searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow
   ******************************************************************************
     filename : /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155/modules/elbow/flowchart.py FOUND
   ******************************************************************************
   searching: /usr/local/apps/Phenix/1.10.1-2155/phenix-1.10.1-2155
   searching: /home/dyda/.elbow
   searching: /home/dyda
   searching: /spin1/users/dyda/myligand


        Machine has   24018 Mb total memory
                      14687 Mb free memory 
        Setting        1000 Mb max memory usage

 Searching for template run file: GAMESS.csh
   searching: /spin1/users/dyda/myligand
   ******************************************************************************
     filename : /spin1/users/dyda/myligand/GAMESS.csh  FOUND
   ******************************************************************************

 Using /spin1/users/dyda/myligand/GAMESS.csh as input run file template

all .inp, .dat, .gam files are produced, no errors, but no cif file.

Thanks.

Fred
*******************************************************************************
Fred Dyda, Ph.D.                       Phone:301-402-4496
Laboratory of Molecular Biology        Fax: 301-496-0201
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