[Dock-fans] message in amber score

liane saiz liane at uclv.edu.cu
Mon Apr 28 09:05:36 PDT 2008


Hi everyone!!
I was running the dock6 amber scoring function when the following sign
appeared in my screen:

select_atoms: atom-expr too complicated

the Amber parameters I used were as follow


Amber Score Parameters
------------------------------------------------------------------------------------------
amber_score_primary                                          yes
amber_score_secondary                                        no
amber_score_receptor_file_prefix
Model_1_min_chimera
amber_score_movable_region                                   distance
amber_score_movable_distance_cutoff                          10
receptor_site_file                               Model_1_min_chimera.sph
amber_score_before_md_minimization_cycles                    100
amber_score_md_steps                                         3000
amber_score_after_md_minimization_cycles                     100
amber_score_gb_model                                         5
amber_score_nonbonded_cutoff                                 18.0
amber_score_temperature                                      300.0

the calculations are still in progress but I don't know whether they are
reliable since I've ever seen this message before. Could somebody kindly
tell me more about this??
Previous calculations with amber_score_movable_region=ligand were
succesfully completed with no strange messages.
thanks in advance
Liane

Servicio de Correos de la Universidad Central "Marta Abreu" de Las Villas. http://www.uclv.edu.cu
-VI Conferencia Internacional de Ciencias Empresariales, del 16 al 18 de octubre de 2008, Cayo Santa María, Cuba. http://economia-publica.uab.es/VIcubaCICE.doc
-V Conferencia Científica Internacional de Ingeniería Mecánica, COMEC 2008, del 4 al 6 de noviembre de 2008,  UCLV, Cuba. http://eventos.fim.uclv.edu.cu/comec


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