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:
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
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
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
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
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
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
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?
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