[gmx-users] free energy calculations for reference state for constant pH MD simulations...

[Mehmet Ozbil]

Now I successfully ( I believed so) incorporated both protonated and
deprotonated states of GLU residue in the .top file. As I am trying to
energy minimize the system, it gives me an error saying:


WARNING 1 [file GLUTest3_GROMOS_p.top, line 52]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning H bonds into constraints...
Excluding 3 bonded neighbours molecule type 'LIG'
turning H bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning H bonds into constraints...
Coupling 1 copies of molecule type 'Protein_chain_A'

NOTE 1 [file GLUTest3_GROMOS_p.top, line 141]:
  State B has non-zero total charge: -3.770292e-04


What do they mean? What shall I do regarding the non zero charge and more
importantly the missing interactions in state B?

Best,
Mehmet Ozbil

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