<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Hi,<br>Thanks a lot for the reply and the suggestion.<br>I am carrying the simulation in 100% DMSO( no water) at 318 K.the em.mdp file is as follows:<br>
define = -DFLEXIBLE<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; time step<br>nsteps = 1000 ; number of steps<br>nstlist = 10 ; update pairlist<br>
ns_type = grid<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off ;shift<br>rlist = 1.0 ; cut-off for ns<br>rvdw = 1.4<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000<br>
emstep = 0.01<br><br><br><br>DSSP is giving change in the sheet, loop and turn content although the helix content remains the same on comparison with the native pdb. What is more surprising is that though it is a homodimer the structure change in the two monomers is not the same ( in one monomer the sheet is extended while in the other it is not.<br>
Is it fine if I try to first energy minimize the structure in vacuum and then solvate in DMSO box and run the MD without minimizing in DMSO box. </span><span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; ">Also when I am trying any other force field an error is coming 'Atomtype SD not found'.</span><div>
<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "> For check I ran the MD of my protein in water using G43a1 forcefield, in that also after em step the loop is turning into a beta sheet. </span></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Please let me know if there is any manual on DMSO box generation and equilibration. <br></span></font><div>
<span class="Apple-style-span" style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse; "><br>Regards,<br clear="all">Swagata Chakraborty<br>Research Scholar,<br>Department of Chemical Sciences,<br>
Tata Institute of Fundamental Research, <br>Mumbai-400005<br></span>Swagata Chakraborty<br>Research Scholar,<br>Department of Chemical Sciences,<br>Tata Institute of Fundamental Research, <br>Mumbai-400005<br><br>
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