Dear all amber users,
I have made some modifications in a protein by attaching different number
of ligand molecules at selected amino-acid residues. To analyse the effect
of such changes I will be minimizing the system and then running dynamics
on it using the GB model.
I shall be using both amber 7 and 8 to observe the effect of different
number of ligands on the conformation of the protein.
1. Will I get substantial differences while comparing the results abtained
from simulations on amber 7 and amber 8?
2. Will it be acceptable to compare the results obtained in both the
situations, if yes then do I need to take care of some specific flags and
options?
Thanks in adavance for your suggestions,
With best regards,
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Received on Wed Oct 06 2004 - 11:53:00 PDT
