Dear Erik thank for your answer.
my rtp file for amber 03 force field is as follow : [ NGLY ] [ atoms ] N amber99_39 0.29430 1 H1 amber99_17 0.16420 2 H2 amber99_17 0.16420 3 H3 amber99_17 0.16420 4 CA amber99_11 -0.01000 5 HA1 amber99_28 0.08950 6 HA2 amber99_28 0.08950 7 C amber99_2 0.61630 8 O amber99_41 -0.57220 9 and my top file is as follow : [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 amber99_39 1 NGLY N 1 0.2943 14.01 2 amber99_17 1 NGLY H1 2 0.1642 1.008 3 amber99_17 1 NGLY H2 2 0.1642 1.008 4 amber99_17 1 NGLY H3 2 0.1642 1.008 5 amber99_11 1 NGLY CA 3 -0.01 12.01 6 amber99_28 1 NGLY HA1 4 0.0895 1.008 7 amber99_28 1 NGLY HA2 5 0.0895 1.008 8 amber99_2 1 NGLY C 6 0.6163 12.01 9 amber99_41 1 NGLY O 7 -0.5722 16 what relation is there between both of my rtp and top file in above ?
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