Dear Amber users,
I set up a alchemy simulation for the GTG to GAG mutation in water (with head and tail groups neutralized). Following the typical procedure, I did electrostatics first and then vdw. In the vdw alchemy process, I used softcore method. But I got very different dv/dl values when I use
scmask=':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and scmask=':3.CB,HB1,HB2,HB3' for GAG
or
scmask=':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and scmask=':3.HB1,HB2,HB3' for GAG
I can't figure out what is the problem. It seems to me they should give same or at least similar results.
Best,
Lishan
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Received on Thu May 05 2011 - 02:30:02 PDT
