Lingand Unbinding using SMD

From: Jacopo Sgrignani (sgrigna_at_sissa.it)
Date: Mon Aug 15 2011 - 02:19:17 CDT

Dear All
I'm trying to run an SMD simulation to study the ligand unbinding
using explicit solvent, then I modified the input file including these
lines

SMD on
SMDFile ref.pdb
SMDk 7
SMDVel 0.0001
SMDOutputFreq 100
SMDDir 1.15 -0.61 -17.72

In the ref.pdb file I set to 1 the last column only for the CA of the protein:

ATOM 5 CA MET X 1 7.235 -27.749 -57.437 0.00 1.00

and I set to 1 the occupancy column for the ligand atoms:

ATOM 8172 C10 ASD X 500 -2.918 -7.352 22.951 1.00 0.00
ATOM 8173 H12 ASD X 500 -3.159 -7.115 21.937 1.00 0.00
ATOM 8174 H13 ASD X 500 -3.767 -7.894 23.359 1.00 0.00
ATOM 8175 H14 ASD X 500 -2.838 -6.395 23.471 1.00 0.00
ATOM 8176 C5 ASD X 500 -1.582 -8.083 23.104 1.00 0.00
ATOM 8177 C4 ASD X 500 -1.180 -8.204 24.581 1.00 0.00
ATOM 8178 H5 ASD X 500 -0.328 -8.861 24.620 1.00 0.00.....

However the simulation appears strange, because the protein seems to
move and also some water molecules are translated.
Could you suggest me the best way to run this simulation (I'm not able
to find a tutorial for the ligand unbinding).

Thanks a lot

Jacopo

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