[gmx-users] questions about PRODRG

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Fri Nov 22 20:34:43 CET 2002

 Hi everybody!!

If I want to generate a topology with PRODRG, what is better?? taking the coordinates from the crystal structure of the small molecule (from the Cambridge database),

or taking the coordinates of the ligand (the one in the binded conformation) from the crystal structure of the complex protein-ligand. Have I to take into account the resolution to choose one of theese??

Another question: coordinates from the crystal structure of the ligand (from the ligand-protein complex ) at medium resolution (3.0-3.5 A) are OK for PRODRG

or does it need higher resolution?? I mean, is the resolution a so critical factor for PRODRG?? (I read in the paper for PRODRG that it was, but I ask how big is it??)

Thans in advance for your kind attention,

with best regards,



Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380

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