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