[gmx-users] [gmx-users]Violation of distance restraints

Chris de graaf degraaf at few.vu.nl
Mon Sep 8 09:57:00 CEST 2003

Dear gmx'ers, 
I am trying to use 7 spin relaxation NMR derived distance restraints between atoms of a small organic molecule (substrate) and a protein to refine a substrate-enzyme complex with MD. As a starting structure, I use a automaticaly docked substrate pose in the protein binding pocket which is more or less in agreement with these distance restraints.  However, as the substrate and the protein are not considered as one molecule,  the distance restraints are 'heavily violated' (31 nm!) as a result of the fact that the substrate is 'placed outside' the protein ('placed outside the box'), and the run crashes immediately. 

I want to solve this problem by defining either one 'connection bond' or one 'harmonic potential bond' (with a force constant of "0") between the substrate and the protein (in addition to the distance restraints), because I do not want to turn these bonds into constraints, and I do not  want to define a 'chemical' bond between the protein and the substrate. Which bond type should I use? 

With kind regards and thanking you in advance, 


C. de Graaf, MSc 

LACDR - Division of Molecular Toxicology 
Department of Pharmacochemistry, 
Vrije Universiteit, 
De Boelelaan 1083, 1081 HV Amsterdam

Tel. (31) 020-4447608
Fax. (31) 020-4447610
email: degraaf at few.vu.nl  
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