[gmx-users] strange new H-H bond formation during MD
Mark.Abraham at anu.edu.au
Tue Oct 24 17:33:18 CEST 2006
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.
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