Re: [gmx-users] top2psf with Amber99SB-ILDN

2012-11-22 Thread francesco oteri
yes,actually it works fine as long as you have one chain in you .top file . if u have more subunits, u are supposed to merge the chains using the appropriate value for -chainsep option in pdb2gmx 2012/11/22, Steven Neumann : > There was an error with index < 1 which this script assigned to bond >

Re: [gmx-users] top2psf with Amber99SB-ILDN

2012-11-22 Thread Steven Neumann
There was an error with index < 1 which this script assigned to bond part. The script provided here: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/top2psf.pl works much better. Steven On Thu, Nov 22, 2012 at 12:50 PM, francesco oteri wrote: > hi,it would be nice knowing th

Re: [gmx-users] top2psf with Amber99SB-ILDN

2012-11-22 Thread francesco oteri
hi,it would be nice knowing the errors. Francesco 2012/11/22, Steven Neumann : > Dear Gmx Users, > > Is it possible to convert topology produced by Gmx and convert it ont > the psf file? I used Justin script but when I load pdb and psf in VMD > then there are some errors. > Would you help? > > S