Re: Lingand Unbinding using SMD

From: Jian Liu (bay__gulf618_at_163.com)
Date: Mon Aug 15 2011 - 03:28:37 CDT

Dear Jacopo
Have you constrainted the COM of the protein?
If not, when you steer the ligand off the protein, the protein would also be shuffled away.
Two superiorer methods as follow: One is to use the smd.tcl script attached in 10Ala tutorial, http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/; The other iscolvar.

--
¡¡ Jian Liu
¡¡ PhD Graduate Candidate in SINAP,Chin Ac Sci
At 2011-08-15 15:19:17,"Jacopo Sgrignani" <sgrigna_at_sissa.it> wrote:
>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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