[gmx-users] help with molecules not in the database

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 14 19:21:12 CET 2008

rahmanm at queensu.ca wrote:
> Hello all,
> I'm very new to Gromacs and am trying to do a simple energy minimization 
> (potentially doing the full mds later).  However, at the first step 
> (pdb2gmx) I get a fatal error as there is apparently no AMP in the 
> database.  The molecule contains both AMP and Fructose-6-phosphate.  I 
> have gone to the Dundee PRODGR server and generated a Gromacs topology 
> file for AMP but I'm not entirely sure how to use it.  Does it go in the 
> forcefield .rtp file?  The format of what I generated is a bit different 
> than that.  Is there a way to use it as a separate entity?  Any help or 
> direction would be greatly appreciated ;-)

PRODRG will give you a topology (.top) that can be included in your system 
topology as an .itp file.  A thorough understanding of Chapter 5 of the manual 
is required if you don't understand the file types and how they are used.  There 
are also several good tutorials online for getting used to Gromacs and how it 
works, just do a simple Google search.

A caveat about PRODRG - the charges and charge groups it assigns are often 
unsatisfactory, requiring manual alteration.  Parameterization of new species is 
very laborious.  See the wiki page for more information, and read the primary 
literature pertaining to the force field you want to use.


> Thank you
> Mona Rahman
> ---------------------------------------------------
> Mona N. Rahman, Ph.D.
> Dept. of Biochemistry/Pharmacology & Toxicology
> Botterell Hall, Rooms 623 and 634 (lab)
> Queen's University, Kingston, ON, K7L 3N6
> Phone:  613-533-2993, 613-533-6293 (lab)
> E-mail:  rahmanm at queensu.ca
> ------------------------------------------------------------------------
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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