[gmx-users] Bond type for GROMOS !!
ritwik kavathekar
kavathekar_r at yahoo.co.in
Fri Mar 10 13:04:57 CET 2006
Hi,
sorry for posting the doubt on the wrong email Erick.
How does one get gromos atom types for a new system. I
am using GROMACS ver 3.3, G43a2 force field, on a
lipid system pasted below...
Ritwik Kavathekar
Theoretical Chemistry Group,
University of Pune
INDIA
http://chem.unipune.ernet.in/tcg.html
ATOM 1 C1 CE1 1 7.620 2.366 -0.639
1.00 0.00
ATOM 2 C2 CE1 1 6.214 2.049 -1.178
1.00 0.00
ATOM 3 C3 CE1 1 5.162 2.443 -0.127
1.00 0.00
ATOM 4 C4 CE1 1 3.756 2.123 -0.662
1.00 0.00
ATOM 5 C5 CE1 1 2.713 2.520 0.395
1.00 0.00
ATOM 6 C6 CE1 1 1.303 2.197 -0.124
1.00 0.00
ATOM 7 C7 CE1 1 0.273 2.598 0.943
1.00 0.00
ATOM 8 C8 CE1 1 -1.142 2.263 0.448
1.00 0.00
ATOM 9 C9 CE1 1 -2.160 2.658 1.529
1.00 0.00
ATOM 10 C10 CE1 1 -3.573 2.293 1.055
1.00 0.00
ATOM 11 C11 CE1 1 -4.591 2.663 2.146
1.00 0.00
ATOM 12 C12 CE1 1 -5.987 2.236 1.679
1.00 0.00
ATOM 13 C13 CE1 1 -7.030 2.549 2.764
1.00 0.00
ATOM 14 C14 CE1 1 -8.346 2.038 2.282
1.00 0.00
ATOM 15 C15 CE1 1 -9.417 2.025 3.071
1.00 0.00
ATOM 16 C16 CE1 1 -10.686 1.458 2.520
1.00 0.00
ATOM 17 OAA CE1 1 -10.627 1.512 1.093
1.00 0.00
ATOM 18 HAA CE1 1 -10.551 2.465 0.799
1.00 0.00
ATOM 19 C17 CE1 1 -10.803 -0.013 2.970
1.00 0.00
ATOM 20 C18 CE1 1 -12.081 -0.682 2.420
1.00 0.00
ATOM 21 OAB CE1 1 -12.023 -0.719 0.994
1.00 0.00
ATOM 22 HAB CE1 1 -12.850 -1.152 0.638
1.00 0.00
ATOM 23 N1 CE1 1 -9.685 -0.726 2.476
1.00 0.00
ATOM 24 HAC CE1 1 -9.155 -0.363 1.710
1.00 0.00
ATOM 25 C19 CE1 1 -9.329 -1.940 3.067
1.00 0.00
ATOM 26 OB CE1 1 -10.058 -2.416 3.947
1.00 0.00
ATOM 27 C20 CE1 1 -8.061 -2.678 2.686
1.00 0.00
ATOM 28 C21 CE1 1 -7.052 -1.789 1.920
1.00 0.00
ATOM 29 C22 CE1 1 -5.758 -2.612 1.704
1.00 0.00
ATOM 30 C23 CE1 1 -4.632 -1.743 1.094
1.00 0.00
ATOM 31 C24 CE1 1 -3.346 -2.604 0.988
1.00 0.00
ATOM 32 C25 CE1 1 -2.148 -1.756 0.498
1.00 0.00
ATOM 33 C26 CE1 1 -0.878 -2.643 0.457
1.00 0.00
ATOM 34 C27 CE1 1 0.360 -1.808 0.051
1.00 0.00
ATOM 35 C28 CE1 1 1.618 -2.713 0.038
1.00 0.00
ATOM 36 C29 CE1 1 2.877 -1.882 -0.314
1.00 0.00
ATOM 37 C30 CE1 1 4.128 -2.798 -0.330
1.00 0.00
ATOM 38 C31 CE1 1 5.395 -1.964 -0.649
1.00 0.00
ATOM 39 C32 CE1 1 6.643 -2.885 -0.687
1.00 0.00
ATOM 40 C33 CE1 1 7.913 -2.047 -0.989
1.00 0.00
ATOM 41 C34 CE1 1 9.157 -2.970 -1.058
1.00 0.00
ATOM 42 C35 CE1 1 10.426 -2.127 -1.350
1.00 0.00
ATOM 43 C36 CE1 1 11.670 -3.048 -1.451
1.00 0.00
ATOM 44 C37 CE1 1 12.934 -2.195 -1.735
1.00 0.00
ATOM 45 C38 CE1 1 14.182 -3.108 -1.868
1.00 0.00
ATOM 46 C39 CE1 1 15.438 -2.243 -2.142
1.00 0.00
ATOM 47 C40 CE1 1 16.690 -3.143 -2.301
1.00 0.00
ATOM 48 C41 CE1 1 17.938 -2.262 -2.563
1.00 0.00
ATOM 49 C42 CE1 1 19.198 -3.146 -2.743
1.00 0.00
ATOM 50 C43 CE1 1 20.433 -2.244 -2.990
1.00 0.00
ATOM 51 C44 CE1 1 21.706 -3.105 -3.190
1.00 0.00
ATOM 52 C45 CE1 1 22.923 -2.176 -3.419
1.00 0.00
ATOM 53 C46 CE1 1 24.214 -3.004 -3.635
1.00 0.00
ATOM 54 C47 CE1 1 25.406 -2.040 -3.843
1.00 0.00
ATOM 55 C48 CE1 1 26.719 -2.825 -4.074
1.00 0.00
ATOM 56 OC CE1 1 27.795 -1.888 -4.251
1.00 0.00
ATOM 57 C49 CE1 1 29.008 -2.549 -4.476
1.00 0.00
ATOM 58 OD CE1 1 29.049 -3.785 -4.507
1.00 0.00
ATOM 59 C50 CE1 1 30.266 -1.743 -4.684
1.00 0.00
ATOM 60 C51 CE1 1 31.477 -2.671 -4.927
1.00 0.00
ATOM 61 C52 CE1 1 32.741 -1.806 -5.132
1.00 0.00
ATOM 62 C53 CE1 1 33.969 -2.705 -5.389
1.00 0.00
ATOM 63 C54 CE1 1 35.220 -1.821 -5.591
1.00 0.00
ATOM 64 C55 CE1 1 36.449 -2.713 -5.859
1.00 0.00
ATOM 65 C56 CE1 1 37.702 -1.833 -6.065
1.00 0.00
ATOM 66 C57 CE1 1 38.889 -2.723 -6.331
1.00 0.00
ATOM 67 C58 CE1 1 40.103 -2.215 -6.547
1.00 0.00
ATOM 68 C59 CE1 1 40.347 -0.730 -6.533
1.00 0.00
ATOM 69 C60 CE1 1 41.803 -0.476 -6.822
1.00 0.00
ATOM 70 C61 CE1 1 42.297 0.763 -6.852
1.00 0.00
ATOM 71 C62 CE1 1 41.419 1.956 -6.598
1.00 0.00
ATOM 72 C63 CE1 1 42.267 3.237 -6.693
1.00 0.00
ATOM 73 C64 CE1 1 41.379 4.466 -6.431
1.00 0.00
ATOM 74 C65 CE1 1 42.234 5.743 -6.527
1.00 0.00
ATOM 75 C66 CE1 1 41.348 6.975 -6.265
1.00 0.00
TER
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