Hi,
two things:
a) Are you talking about deltaG values from one transformation? These will
certainly be different. Only deltadeltaG values from a properly set up
thermodynamic cycle will give interpretable results.
b) If you do get very different ddG values, this indicates that your
simulation is not converged. You don't give simulation details, so it's
impossible to judge that.
Kind Regards,
Thomas
On Thu, May 5, 2011 5:29 am, Lishan Yao wrote:
> 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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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu May 05 2011 - 04:00:03 PDT
