On Thu, Nov 25, 2010 at 9:49 AM, Almus <almupino.gmail.com> wrote:
> 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!
>
This is because this atom is NOT in your amber prep file (which is what you
want, correct?). H42 is not in the amber prep file, so it is not given a
type in the ALE residue. If you are loading a PDB with an ALE residue in
it, that PDB likely has the H42 atom, which is not mapped to anything by the
Amber prep file you created, thus giving this error.
If you WANT that hydrogen atom in your system, you'll have to remake the
amber prep file with that hydrogen. If you do NOT want that hydrogen atom
in your system, then just remove the offending H42 from your PDB file and it
should work just fine.
Good luck!
Jason
> --
> Almudena Pino
> Universidad de Málaga.
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Nov 25 2010 - 08:30:02 PST
