Dear Justin, Thank you so much for your help. Could you please help me with some simple questions:
1- Regarding the atom types: For n-Hexane why did not you choose atom types: opls_068 15.03500 ; CH3 (C2) N-ALKANES opls_071 14.02700 ; CH2 (SP3) ALKANES rather than: opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols opls_158 12.01100 ; all-atom C: CH, alcohols I would like to know the reason because I am confused which type to pick up. 2-Please tell me what the difference between atom type C and CA is? [ HEX ] [ atoms ] CAA opls_157 -0.180 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 HA3 opls_140 0.060 1 CAC opls_158 -0.120 2 HC1 opls_140 0.060 2 HC2 opls_140 0.060 2 CAE opls_158 -0.120 3 HE1 opls_140 0.060 3 HE2 opls_140 0.060 3 CAF opls_158 -0.120 4 HF1 opls_140 0.060 4 HF2 opls_140 0.060 4 CAD opls_158 -0.120 5 HD1 opls_140 0.060 5 HD2 opls_140 0.060 5 CAB opls_157 -0.180 6 HB1 opls_140 0.060 6 HB2 opls_140 0.060 6 HB3 opls_140 0.060 6 [ bonds ] CAA HA1 CAA HA2 CAA HA3 CAA CAC CAC HC1 CAC HC2 CAC CAE CAE HE1 CAE HE2 CAE CAF CAF HF1 CAF HF2 CAF CAD CAD HD1 CAD HD2 CAD CAB CAB HB1 CAB HB2 CAB HB3 3- Regarding pdb file: 3-1-How did you create this pdb file? 3-2- Why HETATM rather than ATOM? I searched for HETATM and ATOM and I found this: ATOM:Atomics coordinate records for standard groups HETATM: Atomics coordinate records for heterogens What does this mean? 4-In my Pdb file I had zero numbers for the last two columns. What is the reason for 1 and 20 figures in this pdb file? 5-and finally, do I need to add the rtp file to ffoplsaa.rtp in share/gromacs/top directory? Thank you for your help and time in advance. :) (in conjunction with the following .pdb file): HETATM 1 CAA HEX 1 8.330 1.510 -0.010 1.00 20.00 C HETATM 2 HA1 HEX 1 9.281 1.200 -0.024 1.00 20.00 H HETATM 3 HA2 HEX 1 8.154 2.080 -0.813 1.00 20.00 H HETATM 4 HA3 HEX 1 8.166 2.044 0.820 1.00 20.00 H HETATM 5 CAC HEX 1 7.400 0.300 -0.030 1.00 20.00 C HETATM 6 HC1 HEX 1 7.584 -0.267 0.773 1.00 20.00 H HETATM 7 HC2 HEX 1 7.573 -0.231 -0.860 1.00 20.00 H HETATM 8 CAE HEX 1 5.940 0.730 -0.010 1.00 20.00 C HETATM 9 HE1 HEX 1 5.754 1.291 -0.816 1.00 20.00 H HETATM 10 HE2 HEX 1 5.769 1.266 0.817 1.00 20.00 H HETATM 11 CAF HEX 1 5.010 -0.480 -0.020 1.00 20.00 C HETATM 12 HF1 HEX 1 5.192 -1.038 0.790 1.00 20.00 H HETATM 13 HF2 HEX 1 5.186 -1.020 -0.843 1.00 20.00 H HETATM 14 CAD HEX 1 3.540 -0.050 -0.010 1.00 20.00 C HETATM 15 HD1 HEX 1 3.357 0.507 -0.820 1.00 20.00 H HETATM 16 HD2 HEX 1 3.363 0.489 0.813 1.00 20.00 H HETATM 17 CAB HEX 1 2.610 -1.270 -0.020 1.00 20.00 C HETATM 18 HB1 HEX 1 1.658 -0.964 -0.013 1.00 20.00 H HETATM 19 HB2 HEX 1 2.780 -1.812 -0.843 1.00 20.00 H HETATM 20 HB3 HEX 1 2.785 -1.830 0.790 1.00 20.00 H
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