Hello. Ie been trying to run a DNA simulation with gromacs using amber99 force field. I've started with my DNA sequence complexed with the protein, but then decided to separate them to know exactly what the problem was. Now I am not even using the DNA sequence from my pdb file. I`ve used the NAB server to create a DNA sequence which is exactly the same as the one I had. I decided to do this in order to minimize the problems with the amber forcefield. Well, that didn't work either. I keep getting the "Error - No default Bond types.....no default angle types....etc " On a previous email I asked the same question, and the answer was. Take a look at the lines where the error appears. Just to be more specific on my problem.....ERROR 0 [file "1vkxdna_C.itp", line 71]: No default Bond types ERROR 0 [file "1vkxdna_C.itp", line 196]: No default Angle types Ok. I've taken the last advice and went ther to line 196. Except that on line 196 there are 4 columns "16 18 19 1" with values that I cannot spot the problem. I went to the manual to see what each line means but came out without knowing exactly what to do with them. Another problem I've spotted is that the charge (no matter what i try) always comes out as a non integral value. I've renamed all atoms exactly like they should be...one by one....really...one by one. I would like some advice on the problem if possible.
Ps: The amber Dickerson test works out just fine.
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