Hi All
this is what i tried , am sorry if i should not be talking about the gomacs here but i tried these steps , then converting back to pdb and using the pdb files to run lammps. because i want to use a specific water in lammps.
i tried doing the steps using gromacs by making the top file , and using the genbox to create a box and include the protein.pdb file in it but it did not work (step 1), so i converted the pdb to gro file and then did the step again using the genbox , this time it worked but the out file looked strange in the vmd . i proceeded with the gro file to minimization and then to use the minimized gro file which is the protein in the box and solvate using genbox again , this time the command will not give me any results , no out put , it will just freesze the screen and when i stop the process , it print on screen that the command is stopped
thank you
these are the steps
-
- genbox -ci bb.pdb -nmol 1 -box 7.7 7.7 7.7 -try 50 -o bb.pdb
- minimize the system