Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-20 Thread Kwee Hong
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

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-20 Thread Justin A. Lemkul
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

[gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Kwee Hong
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

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Justin A. Lemkul
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

Re: [gmx-users] top2psf.pl is generating some bonds to atoms with index 0.

2010-10-19 Thread Justin A. Lemkul
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