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: [EMAIL PROTECTED]
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