hello every Amber-user,
I have simulated a complex composed of three moleculares of protein and one molecular of DNA.Now I got the complex's trajectory and want to calculate each protein's contribution to the total binding energy of the interaction of the proteins and DNA.
Now the question is how to set the parameters of the MM_PBSA tutorial's extracting coordinate script.Specially speaking,I don't know how to deal with the
NUMBER_LIG_GROUPS and the NUMBER_REC_GROUPS.In my opinion,as I want to calculate the single protein's contribution,I have to set this very protein to receptor or ligand,and let the remains to be the ligand or receptor.For example,if my complex has 100 atoms totally and composed like this:DNA:1-10 atom,protein A:11-40 atom,protein B:41-70,protein C:71-100.If now I want to konw the detailed contribution of protein A,so in the NUMBER_LIG_GROUPS item,I can set it like this,
NUMBER_LIG_GROUPS 1
LSTART 11
LSTOP 40
now,the question appears,that is how to deal with the NUMBER_REC_GROUPS item.The remained moleculars is not single one and the atoms are obviously not consecutive.So does anybody know how to figure it out?
Many thanks!
2010-05-08
geyan
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Received on Sat May 08 2010 - 09:30:04 PDT
