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
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