Dear Amber users
I am a research Scholar who is working on biomolecular modelling.
As am a beginner,I just started some homology modelling studies.
I have a doubt.While building a structure,for doing MD simulations will the
small bond lengths difference cause problems in the simulation?
I mean is thre any problem if we fix the bond lenghts as 1.48 instead of
1.49?
Will that cause a very major problem in the simulation?
I have built a model of a biomolecule.As I cant break the benzene ring I
didnt make any difference in the benzene ring part.
i just changed some atoms which is connected to benzene ring.
But in the benzene ring the bond lengths are slightly different for the
model which I am supposed to make and the model which I am making
modifications.
When I done simulations with this structure,it showed some problems such as
velocity limit exceeded etc.
Is that because of this bond length problem?
regards
Aparna
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Received on Sun Oct 02 2011 - 23:00:02 PDT
