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

[rahmanm at queensu.ca]

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 ;-)

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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