[gmx-users] How to build caps for my peptide termini?

[Apramita Chand]

Dear All,
I want to cap the ends of my peptide chain. Though -ter option of pdb2gmx
takes up its zwitterionic form quite easily, I've read somewhere that
termini are quite mobile and it is better to proceed with capping. I want
to use GROMOS53a6 parameters and I've found entries of ACE and NAC in its
.rtp file. My dilemma is how to build caps onto my pdb file? What about
their coordinates? Where should I insert them? I tried building it using
pymol but it didn't work. Some softwares like Schrodinger's Protein
Preparation Wzard is great with stuff like this but I don't have the
resources to buy paid software. Could you please suggest a way how to do
this?
Here are some of the coordinates
Starting residue:

ATOM      1  N   GLN A   1       7.066  21.384  0.641  1.00 11.02           N
ATOM      2  CA  GLN A   1       5.949  20.973  1.534  1.00 10.36           C
ATOM      3  C   GLN A   1       5.275  19.686  1.047  1.00  9.45           C
ATOM      4  O   GLN A   1       5.014  18.782  1.840  1.00  9.34           O
ATOM      5  CB  GLN A   1       4.928  22.115  1.616  1.00 10.69           C
ATOM      6  CG  GLN A   1       3.676  21.765  2.403  1.00 11.26           C
ATOM      7  CD  GLN A   1       3.987  21.223  3.784  1.00 11.68           C
ATOM      8  OE1 GLN A   1       3.745  20.021  4.019  1.00 11.97           O
ATOM      9  NE2 GLN A   1       4.475  22.002  4.632  1.00 11.90           N
ATOM     10  H1  GLN A   1       7.823  21.771  1.239  1.00 11.21           H
ATOM     11  H2  GLN A   1       6.702  22.105 -0.016  1.00 11.26           H
ATOM     12  H3  GLN A   1       7.392  20.540  0.130  1.00 11.19           H
ATOM     13  HA  GLN A   1       6.354  20.797  2.521  1.00 10.53           H
ATOM     14  HB2 GLN A   1       5.397  22.965  2.088  1.00 10.93           H
ATOM     15  HB3 GLN A   1       4.631  22.391  0.615  1.00 10.52           H
ATOM     16  HG2 GLN A   1       3.073  22.656  2.510  1.00 11.34           H
ATOM     17  HG3 GLN A   1       3.119  21.019  1.857  1.00 11.54           H

Ending residue

ATOM    475  N   LEU A  33      -9.783 -18.497 -1.487  1.00  5.97           N
ATOM    476  CA  LEU A  33     -10.736 -19.453 -0.936  1.00  6.85           C
ATOM    477  C   LEU A  33     -10.018 -20.571 -0.187  1.00  7.51           C
ATOM    478  O   LEU A  33     -10.708 -21.452  0.366  1.00  7.81           O
ATOM    479  CB  LEU A  33     -11.601 -20.043 -2.052  1.00  7.27           C
ATOM    480  CG  LEU A  33     -12.071 -19.040 -3.107  1.00  7.87           C
ATOM    481  CD1 LEU A  33     -12.991 -19.715 -4.113  1.00  8.08           C
ATOM    482  CD2 LEU A  33     -12.773 -17.862 -2.446  1.00  8.48           C
ATOM    483  OXT LEU A  33      -8.769 -20.557 -0.163  1.00  7.98           O
ATOM    484  H   LEU A  33      -9.837 -17.556 -1.214  1.00  5.99           H
ATOM    485  HA  LEU A  33     -11.373 -18.923 -0.242  1.00  7.08           H
ATOM    486  HB2 LEU A  33     -11.031 -20.815 -2.548  1.00  7.07           H
ATOM    487  HB3 LEU A  33     -12.473 -20.495 -1.604  1.00  7.69           H
ATOM    488  HG  LEU A  33     -11.213 -18.661 -3.642  1.00  8.04           H
ATOM    489 HD11 LEU A  33     -12.516 -20.606 -4.494  1.00  8.27           H
ATOM    490 HD12 LEU A  33     -13.192 -19.036 -4.928  1.00  8.16           H
ATOM    491 HD13 LEU A  33     -13.920 -19.979 -3.629  1.00  8.27           H
ATOM    492 HD21 LEU A  33     -12.052 -17.087 -2.232  1.00  8.84           H
ATOM    493 HD22 LEU A  33     -13.234 -18.189 -1.527  1.00  8.47           H
ATOM    494 HD23 LEU A  33     -13.531 -17.476 -3.112  1.00  8.84           H


yours sincerely

Apramita