Re: Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-20 Thread Mark Abraham
On Mon, May 20, 2013 at 4:36 AM, David Rosenman davidjrosen...@gmail.comwrote: Hello again, Sorry for the delay in my response. The original top file is: http://wikisend.com/download/951610/APPTM_WT.top The grompp -pp processed top is:

Re: Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-19 Thread David Rosenman
chains .itp file. Stephan *Gesendet:* Freitag, 17. Mai 2013 um 16:17 Uhr *Von:* Mark Abraham mark.j.abra...@gmail.com *An:* Discussion list for GROMACS users gmx-users@gromacs.org *Betreff:* Re: [gmx-users] Expanding a .top file to have all connection information How does grompp -pp look

Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-19 Thread Justin Lemkul
On 5/19/13 10:36 PM, David Rosenman wrote: Hello again, Sorry for the delay in my response. The original top file is: http://wikisend.com/download/951610/APPTM_WT.top The grompp -pp processed top is: http://wikisend.com/download/851584/APPTM_WT_processed.top The connectivities that are

Aw: Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-18 Thread lloyd riggs
Or just do it by hand and replace the lines in the .top with each protein chains .itp file. Stephan Gesendet:Freitag, 17. Mai 2013 um 16:17 Uhr Von:Mark Abraham mark.j.abra...@gmail.com An:Discussion list for GROMACS users gmx-users@gromacs.org Betreff:Re: [gmx-users] Expanding a .top file

[gmx-users] Expanding a .top file to have all connection information

2013-05-17 Thread davidjrosenman
Hello everyone, This may be a bit out of the purview of this list, but it can't hurt to ask. Let me start from the beginning: I'm trying to take a structure/topology that I generated with GROMACS tools and convert it to run with NAMD. The problem is that this is a huge simulation box with many

Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-17 Thread Mark Abraham
How does grompp -pp look? Mark On Fri, May 17, 2013 at 3:40 PM, davidjrosenman davidjrosen...@gmail.comwrote: Hello everyone, This may be a bit out of the purview of this list, but it can't hurt to ask. Let me start from the beginning: I'm trying to take a structure/topology that I

Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-17 Thread David Rosenman
This is a good idea, but it doesn't work. It produces a more detailed .top file with force field parameters, but still, only the connectivities of the protein are provided. top2psf has no idea what to do with this file, by the way. Would it help for me to provide the pre-processed and

Re: [gmx-users] Expanding a .top file to have all connection information

2013-05-17 Thread Mark Abraham
On Fri, May 17, 2013 at 4:28 PM, David Rosenman davidjrosen...@gmail.comwrote: This is a good idea, but it doesn't work. It produces a more detailed .top file with force field parameters, but still, only the connectivities of the protein are provided. What connectivities are missing?