[gmx-users] Triple helix built by THeBuScr can not transform by pdb2gmx in Gromacs

[Tsjerk Wassenaar]

Hi Ming Tan,

There is no CD in the rtp entry, just as the message says. There is CD2
though. You can convert the name in your PDB file:

sed '/CD  HYP/CD2 HYP/' input.pdb > output.pdb

Hope it helps,

Tsjerk


On Wed, Mar 4, 2015 at 12:06 PM, Ming Tang <m21.tang at qut.edu.au> wrote:

> Dear all,
> I built an triple helix using the THeBuScr, and used pdb2gmx (with -ignh)
> to get the .top file in GROMACS. But it emerged fatal error:
> Atom CD in residue HYP 12 was not found in rtp entry HYP with 15 atoms
> while sorting atoms.
> I have tried every kind of force field but those including HYP residual
> emerged the same error.
>
> Atoms in triple helix pdb file:
> ATOM     86  N   HYP A  12      30.850  -3.083   2.256  1.00  0.00
>    N
> ATOM     87  CA  HYP A  12      32.080  -2.296   2.141  1.00  0.00
>    C
> ATOM     88  C   HYP A  12      32.710  -2.496   0.763  1.00  0.00
>    C
> ATOM     89  O   HYP A  12      32.550  -3.518   0.123  1.00  0.00
>    O
> ATOM     90  CB  HYP A  12      32.970  -2.847   3.254  1.00  0.00
>    C
> ATOM     91  CG  HYP A  12      32.015  -3.467   4.236  1.00  0.00
>    C
> ATOM     92  CD  HYP A  12      30.918  -4.039   3.374  1.00  0.00
>    C
> ATOM     93  OD  HYP A  12      31.492  -2.476   5.095  1.00  0.00
>    O
>
> Atoms in amber03 aminoacids.tpr
> [ HYP ] ;
> [ atoms ]
>      N    N           -0.25480     1
>    CD2    CT           0.05950     2
>   HD21    H1           0.07000     3
>   HD22    H1           0.07000     4
>     CG    CT           0.04000     5
>     HG    H1           0.04160     6
>    OD1    OH          -0.61340     7
>    HD1    HO           0.38510     8
>     CB    CT           0.02030     9
>    HB1    HC           0.04260    10
>    HB2    HC           0.04260    11
>     CA    CT           0.00470    12
>     HA    H1           0.07700    13
>      C    C            0.58960    14
>      O    O           -0.57480    15
> When ignoring H, the heavy atoms in HYP residual match well between the
> pdb file and the aminoacids.tpr
>
> I have got stuck here for almost one months, and hope somebody can give me
> some advices and solutions.
> Thanks very much
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.