Dear Amber users,
I have used Antechamber and parmchk in order to obtain the prep and frcmod of a 41-atoms molecule. In this small molecule there is an double bond between a carbon (C4A) and a nitrogen (N) atom and both of them have one hydrogen atom bonded (H14 and HN respectively). Prep file is correct and assigning the correct atom types, but when I run tleap in order to get the top and crd files for the whole system (enzyme + small molecule), the program adds a new hydrogen atom (H24), bonded to the C4A atom in the imine bond.
I copy here the prep file and the message gave by tleap:
4 ND1 NB M 3 2 1 1.540 111.208 180.000 -0.685200
5 CE1 CR M 4 3 2 1.350 146.722 -179.768 0.392900
6 HE1 H5 E 5 4 3 1.065 126.931 48.094 0.061200
7 NE2 NA M 5 4 3 1.410 111.773 -129.489 -0.321200
8 HE2 H E 7 5 4 0.958 126.939 178.348 0.302100
9 CD2 CW M 7 5 4 1.401 106.396 1.045 -0.240300
10 HD2 H4 E 9 7 5 1.118 121.508 169.645 0.184200
11 CG CC M 9 7 5 1.437 106.584 0.022 0.283300
12 CB CT M 11 9 7 1.488 122.766 -171.031 -0.103900
13 HB1 HC E 12 11 9 1.135 107.297 -51.580 0.112200
14 HB2 HC E 12 11 9 1.125 108.549 58.364 0.063200
15 CA CT M 12 11 9 1.494 114.290 -176.711 0.020600
16 C C B 15 12 11 1.658 108.986 109.413 0.925900
17 O O2 E 16 15 12 1.249 119.075 -3.440 -0.722500
18 OXT O2 E 16 15 12 1.261 117.388 167.459 -0.834100
19 HA H1 E 15 12 11 1.136 110.636 -2.669 0.089200
20 N N2 M 15 12 11 1.461 114.245 -125.842 -0.522800
21 HN H E 20 15 12 1.029 122.311 -39.048 0.486400
22 C4A CM M 20 15 12 1.313 117.754 139.585 0.228200
23 H14 HA E 22 20 15 1.110 120.000 0.000 0.203500
24 C4 CA M 22 20 15 1.487 122.825 178.519 -0.292200
25 C3 C M 24 22 20 1.465 117.887 24.196 0.569000
26 O3 O E 25 24 22 1.260 124.024 -1.822 -0.629400
27 C2 CA M 25 24 22 1.504 117.619 171.155 -0.023400
28 C2A CT 3 27 25 24 1.501 116.956 171.496 -0.079900
29 H21 HC E 28 27 25 1.136 106.743 120.547 0.059900
30 H22 HC E 28 27 25 1.134 106.640 -2.072 0.110400
31 H23 HC E 28 27 25 1.119 114.327 -121.714 0.060400
32 N1 NA M 27 25 24 1.345 117.918 -0.382 -0.358000
33 H1 H E 32 27 25 0.985 123.584 169.370 0.462000
34 C6 CA M 32 27 25 1.384 122.051 0.369 -0.131500
35 H6 H4 E 34 32 27 1.096 117.439 -173.550 0.188300
36 C5 CA M 34 32 27 1.396 124.041 -2.214 0.044200
37 C5A CT M 36 34 32 1.513 116.576 179.982 0.178600
38 H51 H1 E 37 36 34 1.120 109.871 -111.426 0.152700
39 H52 H1 E 37 36 34 1.133 111.953 134.132 0.095800
40 O4P OS M 37 36 34 1.385 113.380 14.187 -0.557800
41 P P M 40 37 36 1.709 114.060 -176.676 1.318700
42 O3P O2 E 41 40 37 1.513 97.922 90.262 -0.216000
43 O1P O2 E 41 40 37 1.499 103.729 -33.380 -0.236900
44 O2P O2 M 41 40 37 1.483 99.839 -149.694 -0.637500
Created a new atom named: H within residue: .R<ALE 952>
After this, top and crd files are not saved cause H42 (the one above) has no type. Anyone has any idea of why is this happening? And if so, how can it solved? Thank you very much in advance!
--
Almudena Pino
Universidad de Málaga.
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Received on Thu Nov 25 2010 - 07:00:02 PST
