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

[Justin Lemkul]

On 3/11/16 5:17 PM, Robert Molt wrote:
> 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.
>

Use Google.  Enter your search term(s) and then "site:mailman-1.sys.kth.se" at 
the end.

> 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)?
>

pdb2gmx only reads a single coordinate file (and a topology doesn't generally 
vary over a trajectory).  See below.

> 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?
>

Since this is the case, you can't use pdb2gmx.  You'll need something to convert 
your custom force field/topology to GROMACS format.  Try ParmEd.  Other 
converters also exist.

Whether or not you *need* a .tpr depends on the type of analysis you're trying 
to do.  Most programs carry on happily with only a coordinate 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
>

More or less, but do look at 
http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================