[gmx-users] strange new H-H bond formation during MD

[Mark Abraham]

Qiao Baofu wrote:
> Yes. Gromacs can only generate the .pdb file without CONNECTION. I think 
> it is not only Gromacs but Material Studio that do like that. For more 
> than 2 molecules, the softwares give only the coordinate data.
> 
> I find a top2psf.tcl file on the website of VMD (Script Library). It is 
> said this script can transfer .top file to .psf file, which can be 
> recognized by VMD.  But I don't know how to use it and the website of 
> VMD doesn't give the instrution how to use it.  :(

Try reading the file - sometimes instructions are there in code 
comments. Try finding general instructions on using the scripts. Try 
asking the VMD mailing list, not the GROMACS mailing list.

Mark