GROMACS version: 2022.1
GROMACS modification: Yes/No
Here post your question
Dear GROMACS users,
I just want to have a conformation on my protein pdb file containing Ace for the start terminus and Nhe as the end terminus capping.
ATOM 1 C ACE A 0 36.294 36.352 16.452 1.00 0.00 C
ATOM 2 O ACE A 0 35.436 35.466 16.556 1.00 0.00 O
ATOM 3 CH3 ACE A 0 37.482 36.400 17.389 1.00 0.00 C
ATOM 4 1HH3 ACE A 0 38.058 35.490 17.304 1.00 0.00 H
ATOM 5 2HH3 ACE A 0 38.115 37.240 17.141 1.00 0.00 H
ATOM 6 3HH3 ACE A 0 37.144 36.507 18.409 1.00 0.00 H
ATOM 7 N MET A 1 36.175 37.247 15.531 1.00 0.00 N
ATOM 8 CA MET A 1 35.051 37.322 14.533 1.00 0.00 C
ATOM 9 C MET A 1 35.043 36.020 13.823 1.00 0.00 C
ATOM 10 O MET A 1 36.105 35.548 13.433 1.00 0.00 O
ATOM 11 CB MET A 1 35.219 38.534 13.564 1.00 0.00 C
ATOM 12 CG MET A 1 35.031 39.897 14.267 1.00 0.00 C
ATOM 13 SD MET A 1 36.390 40.411 15.359 1.00 0.00 S
ATOM 14 CE MET A 1 37.590 40.728 14.033 1.00 0.00 C
ATOM 15 HA MET A 1 34.122 37.437 15.091 1.00 0.00 H
ATOM 16 HB1 MET A 1 34.455 38.455 12.790 1.00 0.00 H
ATOM 17 HB2 MET A 1 36.233 38.507 13.164 1.00 0.00 H
ATOM 18 HG1 MET A 1 34.118 39.755 14.845 1.00 0.00 H
ATOM 19 HG2 MET A 1 34.933 40.594 13.435 1.00 0.00 H
ATOM 20 HE1 MET A 1 38.531 41.064 14.469 1.00 0.00 H
ATOM 21 HE2 MET A 1 37.759 39.811 13.468 1.00 0.00 H
ATOM 22 HE3 MET A 1 37.202 41.499 13.367 1.00 0.00 H
ATOM 23 H1 MET A 1 36.894 37.955 15.475 1.00 0.00 H
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ATOM 3722 N ARG A 237 4.360 49.380 0.389 1.00 0.00 N
ATOM 3723 CA ARG A 237 3.290 49.889 -0.436 1.00 0.00 C
ATOM 3724 C ARG A 237 2.692 48.796 -1.348 1.00 0.00 C
ATOM 3725 O ARG A 237 1.446 48.656 -1.435 1.00 0.00 O
ATOM 3726 CB ARG A 237 3.781 51.036 -1.359 1.00 0.00 C
ATOM 3727 CG ARG A 237 4.211 52.314 -0.608 1.00 0.00 C
ATOM 3728 CD ARG A 237 4.735 53.434 -1.513 1.00 0.00 C
ATOM 3729 NE ARG A 237 3.577 53.897 -2.353 1.00 0.00 N
ATOM 3730 CZ ARG A 237 3.635 54.884 -3.260 1.00 0.00 C
ATOM 3731 NH1 ARG A 237 4.761 55.556 -3.473 1.00 0.00 N1+
ATOM 3732 NH2 ARG A 237 2.567 55.203 -3.986 1.00 0.00 N
ATOM 3733 H ARG A 237 5.065 48.795 -0.036 1.00 0.00 H
ATOM 3734 HA ARG A 237 2.516 50.257 0.237 1.00 0.00 H
ATOM 3735 HB1 ARG A 237 2.947 51.311 -2.005 1.00 0.00 H
ATOM 3736 HB2 ARG A 237 4.658 50.669 -1.892 1.00 0.00 H
ATOM 3737 HG1 ARG A 237 3.328 52.703 -0.101 1.00 0.00 H
ATOM 3738 HG2 ARG A 237 5.028 52.037 0.059 1.00 0.00 H
ATOM 3739 HD1 ARG A 237 5.132 54.261 -0.924 1.00 0.00 H
ATOM 3740 HD2 ARG A 237 5.546 53.078 -2.148 1.00 0.00 H
ATOM 3741 HE ARG A 237 2.690 53.431 -2.225 1.00 0.00 H
ATOM 3742 1HH1 ARG A 237 5.583 55.314 -2.939 1.00 0.00 H
ATOM 3743 2HH1 ARG A 237 4.804 56.288 -4.167 1.00 0.00 H
ATOM 3744 1HH2 ARG A 237 1.707 54.693 -3.848 1.00 0.00 H
ATOM 3745 2HH2 ARG A 237 2.610 55.935 -4.680 1.00 0.00 H
ATOM 3746 N NHE A 238 3.474 48.024 -2.023 1.00 0.00 N
ATOM 3747 H1 NHE A 238 4.476 48.134 -1.954 1.00 0.00 H
ATOM 3748 H2 NHE A 238 3.085 47.308 -2.620 1.00 0.00 H
TER
is this correct starting the Ace as residue number 0?