Hi, I'm kinda new to computational biochemistry. so here are some few questions of mine:
I made an amylase system solvated with NaCl 5M via PACKMOL, and the pdb file of solvated amylase was generated. after that, I tried to simulate the system in gromacs by skipped the making box and solvation step, because I thought the water, Na+, and Cl- ions had been counted in the system. I checked the topol.top and the gro file generated after I use command pdb2gmx of the pdb file which was come from packmol, then, unfortunately I found that the ions and added water had not been counted. I changed the HETATM titles to ION (for Ca rows) and WATER (for HW1 HW2 01 rows) in all rows after the TER row of pdb file generated by packmol, to make sure all the ions and water were counted. but actually, it did not work.
How to use the pdb file which is generated by Packmol in GROMACS and to make sure all the Na+, Cl- ions, and water to be counted in topol.top and the gro file during the simulation?
thanks in advance
Thank you Nebojša Zec
for your crystal clear explanation, it helped a lot!
hi check Charmm gui server . it will do most of this complicated job for you.
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