Alright..
I actually simulated my protein for 5ns. Then I loaded the trajectory file and
.gro file in vmd. Then, I extracted one of the frame and write it into pdb
format, When I open it with vmd, one of the atom from a residue is connected to
another atom in another residue. Things like this
Kwee Hong wrote:
Alright..
I actually simulated my protein for 5ns. Then I loaded the trajectory
file and .gro file in vmd. Then, I extracted one of the frame and write
it into pdb format, When I open it with vmd, one of the atom from a
residue is connected to another atom in another
Hi,
I've got a top2psf.pl script from the web and used it to generate a psf file.
Yet it generated some bonds to atoms with index 0 which should not occur. It
causes VMD cannot load it and had a segmentation fault.
vmd Info) Using plugin psf for structure file /home/birg/Desktop/zz.psf
Kwee Hong wrote:
Hi,
I've got a top2psf.pl script from the web and used it to generate a psf
file. Yet it generated some bonds to atoms with index 0 which should
not occur. It causes VMD cannot load it and had a segmentation fault.
vmd Info) Using plugin psf for structure file
Kwee Hong wrote:
I executed the script at the therminal by typing
perl top2psf.pl -i topol.top -o zz.psf
Here, I attached my input file.
Your topology does not correspond to a MARTINI coarse-grained topology. As
such, probably a bunch of the pattern matching is getting incorrect
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