[gmx-users] How to Search Forums and Creating Binary from Existing Topology/Trajectory File

[Robert Molt]

Good evening,

I have two questions, one general, one specific.

The big question is that I do not understand how to search the GROMACS 
forums efficiently. The search bar on 
(http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List) allows a 
search to be conducted, but the links shown do not seem to be of the 
user forums and are very slow to load when selected. I can see the grand 
list of all messages on 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/) but it's 
not clear to me how to search it for a particular string.

The specific reason I wanted to search the forums was to answer a very 
specific question. I may as well pose it here, as well. I have converted 
an Amber trajectory into the GROMACS form; I have also converted an 
Amber parameter file to a GROMACS form. I would like to create a GROMACS 
binary (tpr file).

1.) From what I have gleamed from tutorials, I need to use a variant of 
the pdb2gmx command (presumably not for a pdb, but for a trajectory)?

2.) I also do not wish to use the methods of various tutorials like 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html) 
in terms of loading an existing force field; the parameters I have were 
developed in-house. I thus would like to load my 
converted-from-Amber-to-Gromacs topology file. Instead of the -ff flag, 
what flag indicates use of an existing parameter file?

3.) An important caveat: I have to use the 4.5 version of Gromacs. I 
hope the commands are all the same, since I know the current version of 
Gromacs is 5.0

Thank you for your time

-- 
Dr. Robert Molt Jr.
r.molt.chemical.physics at gmail.com