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Hi,<br>I am doing a simulation combining amber and Gaff force field (for dopc lipids), this is the first part of my topology file:<br><br>; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009<br><br>[ defaults ]<br>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>1 2 yes 0.5 0.8333<br><br>[ atomtypes ]<br>;name bond_type mass charge ptype sigma epsilon Amb<br> CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860<br> CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094<br> C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860<br> HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000<br> O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100<br> OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104<br> c3 c3 12.0100 -0.12654 A 3.399676e-01 4.577296e-01 ; 1.91 0.1094<br> hc hc 1.0080 0.02245 A 2.649538e-01 6.568880e-02 ; 1.49 0.0157<br> c2 c2 12.0100 -0.15458 A 3.399676e-01 3.598240e-01 ; 1.91 0.0860<br> ha ha 1.0080 0.11146 A 2.599647e-01 6.276000e-02 ; 1.46 0.0150<br> c c 12.0100 0.44800 A 3.399676e-01 3.598240e-01 ; 1.91 0.0860<br> o o 16.0000 -0.47180 A 2.959927e-01 8.786400e-01 ; 1.66 0.2100<br> os os 16.0000 -0.15429 A 3.000018e-01 7.112800e-01 ; 1.68 0.1700<br> h1 h1 1.0080 0.16551 A 2.471358e-01 6.568880e-02 ; 1.39 0.0157<br> p5 p5 30.9700 1.14364 A 3.741781e-01 8.368000e-01 ; 2.10 0.2000<br> n4 n4 14.0100 0.01626 A 3.250004e-01 7.112800e-01 ; 1.82 0.1700<br> hx hx 1.0080 0.08244 A 1.959981e-01 6.568880e-02 ; 1.10 0.0157<br> OW OW 0.00000 0.00000 A 3.16572e-01 6.49775e-01 ; 1.78 0.1553<br> HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000<br> Na Na 0.00000 0.00000 A 2.15954e-01 1.47545e+00 ; 1.21 0.3526<br> Cl Cl 0.00000 0.00000 A 4.83045e-01 5.34924e-02 ; 2.71 0.0128<br><br>When I try to minimize the system, with grompp -f minimizado.mdp -c final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:<br><br>WARNING 1 [file final_system.top, line 19]:<br> Overriding atomtype c<br>WARNING 2 [file final_system.top, line 20]:<br> Overriding atomtype o<br><br>It is like it is not distinguing the capitals for amber and non-capitals for gaff. Does anybody know which can be the cause of these warnings?<br><br>Thank you very much,<br><br>Rebeca Garcia<br>University of Oxford<br><br /><hr />Nuevo Windows Live, un mundo lleno de posibilidades <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Descúbrelo.</a></body>
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