[gmx-users] simple question about rtp and pdb file

[Moeed]

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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