[gmx-users] Re: .pdb to .gro => the atoms are not conneced with

sobereva sobjubao at yahoo.com.cn
Sun Oct 5 12:41:00 CEST 2008


If you only loaded structure file into VMD(such as .pdb/.gro),connecting relationship will determined by distance between atoms automatically,unless the structure file have connecting information.
  When .pdb convert to .gro,connecting information will lost,if the distance between two atoms in .gro is too long,they won't be connected.If you want to connect them,you can use "setbonds" command in console(see VMD ug),or choose "DynamicBonds" in Drawing Method and set "Distance Cutoff" larger.
  Of course,don't forget to check .gro file carefully before.
  ---- Lu Tian
I make .pdb file to .gro file.

With the VMD, the atoms are seen NOT conneced.

Is there any possible errors in my .gro file?


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