[gmx-users] Free Energy Calculations

jorge_quintero at ciencias.uis.edu.co jorge_quintero at ciencias.uis.edu.co
Mon Mar 8 02:26:49 CET 2010

Hello all.

I worked with free energy calculations to obtain some information related
with solvation and binding free energy, analizing two proteins and using
amber94 force field.  But, I have two questions.

1.  When I tried to do a minization energy, I got the following message:

WARNING 1 [file topol_B.itp, line 10531]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Althoug I didn't have problems with that, is this correct for doing
calculations with this warning message?

2.  Otherwise, I'd like to calculate binding energy between the two
proteins employing the same method.  But I don't know if I can run my
calculations with temperature value close to zero.  doesn't it?

I appreciate your support!

Jorge R. Quintero
Universidad Industrial de Santander
Bucaramanga, Santander - Colombia

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