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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