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Dear Users ! <br><br>I have minimized the attached file using the gromacs43a1 and oplsaa force field using spc water molecules <br><br>I have used the following script for generating topology . <br>i minimized for 2000 steps , my doubt is when i rewrite the minimized pdb , in case of oplsaa <br>i was able to get all atoms , but in the case of the gromacs43a1 i am not getting the hydrogen atoms of the protein , <br><br>how to solve this <br><br>here is the steps which i have used <br><br>-------------------------------<br>pdb2gmx -ignh -ff oplsaa -f 1AKI.pdb -o 1AKI_processed.gro -water spc<br>editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 0.9 -bt cubic<br>genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top<br>grompp -f minim.mdp -c 1AKI_solv.gro -p topol.top -o em.tpr<br>mdrun -v -deffnm em<br>trjconv -f em.trr -o min.pdb -s em.tpr ( in this i gave the option 0 for the total system)<br>------------------------------------------------------------------<br>the minim.mdp <br><br><br>define = -DFLEXIBLE<br>constraints = none<br>integrator = steep<br>dt = 0.002 ; ps !<br>nsteps = 2000<br>nstlist = 10<br>ns_type = grid<br>rlist = 1.0<br>coulombtype = PME<br>rcoulomb = 1.0<br>vdwtype = cut-off<br>rvdw = 1.0<br>optimize_fft = yes<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 10.0<br>emstep = 0.01<br>-----------------------------------------------<br><br><br>thanks in advance <br><br> </div></body>
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