[gmx-users] Capping residues

[Sai Pooja]

Follow-up.
It is easy to make it work. Just needed to be more rigorous. Thank you.

On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipooja at gmail.com> wrote:

> I used -ter option and selected "none" for both terminal ends but I still
> get this error:
>
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a
> proper terminal entry.
> For more information and tips for troubleshooting, please check the GROMACS
>  I have used Mark's definitions for capping residues in the rtp file.
>
> In the pdb file, this is what the capping residues look like:
>
> ATOM     33  N   CBX     5       8.609   2.722  18.430  1.00  1.60      FR1
> ATOM     34  H   CBX     5       9.198   3.338  17.946  1.00  0.80      FR1
> ATOM     35 CH3  CBX     5       7.176   2.594  17.895  1.00  2.17      FR1
>
> ATOM      1  CH3 ACE     1      12.782  -0.027  28.022  1.00  2.17      FR1
> ATOM      2  C   ACE     1      12.532  -0.094  26.546  1.00  2.10      FR1
> ATOM      3  O   ACE     1      13.443  -0.213  25.696  1.00  1.60      FR1
>
>
>
>
>
>
> On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> Sai Pooja wrote:
>>
>>> Thanks Marks. I tried it but this is what I get:
>>>
>>> Fatal error:
>>> atom N not found in buiding block 1ACE while combining tdb and rtp
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>> Do I need to edit the aminoacids.n.tdb file as well?
>>>
>>
>> What are you choosing as your termini when running pdb2gmx?  It should be
>> "none," since by capping, you are not choosing a protonation state for the
>> N- and C-termini.
>>
>> -Justin
>>
>>
>>> Pooja
>>>
>>>
>>>
>>> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <mark.abraham at anu.edu.au<mailto:
>>> mark.abraham at anu.edu.au>> wrote:
>>>
>>>
>>>
>>>    ----- Original Message -----
>>>    From: Sai Pooja <saipooja at gmail.com <mailto:saipooja at gmail.com>>
>>>    Date: Friday, July 2, 2010 7:28
>>>    Subject: Re: [gmx-users] Capping residues
>>>    To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>>>    GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>>>
>>>     > I am sorry if I did not frame the question correctly, but putting
>>>    it very simply, is there a way to use capping residues with the
>>>    charmm forcefield if the residues are --COCH3 and NHCH3?
>>>
>>>    Yes - you edit a copy of the .rtp file in your working directory and
>>>    add whatever you want. Here's what I use in CHARMM
>>>
>>>    [ ACE ]
>>>     [ atoms ]
>>>            CH3     CT3     -0.270  0
>>>            HH31    HA      0.090   0
>>>            HH32    HA      0.090   0
>>>            HH33    HA      0.090   0
>>>            C       C       0.510   1
>>>            O       O       -0.510  1
>>>     [ bonds ]
>>>            C       CH3
>>>            C       +N
>>>            CH3     HH31
>>>            CH3     HH32
>>>            CH3     HH33
>>>            O       C
>>>     [ impropers ]
>>>            C       CH3     +N      O
>>>
>>>    [ NAC ]
>>>     [ atoms ]
>>>           N       NH1     -0.470  1
>>>           HN      H       0.310   1
>>>           CH3     CT3     -0.110  1
>>>           HH31    HA      0.090   1
>>>           HH32    HA      0.090   1
>>>           HH33    HA      0.090   1
>>>     [ bonds ]
>>>           -C      N
>>>           N       HN
>>>           N       CH3
>>>           CH3     HH31
>>>           CH3     HH32
>>>           CH3     HH33
>>>
>>>     [ impropers ]
>>>           N       -C      CH3     HN
>>>           -C      CH3     N       -O
>>>
>>>    Mark
>>>    --
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>>>
>>>
>>> --
>>> Quaerendo Invenietis-Seek and you shall discover.
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
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