[gmx-users] Capping residues

[Sai Pooja]

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.
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