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

[Tsjerk Wassenaar]

Oh bugger. A typo, sorry:

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

Cheers,

Tsjerk

On Wed, Mar 4, 2015 at 12:29 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
>
>


-- 
Tsjerk A. Wassenaar, Ph.D.