[gmx-users] Capping residues
Justin A. Lemkul
jalemkul at vt.edu
Sat Jul 3 22:41:10 CEST 2010
Sai Pooja wrote:
> Follow-up.
> It is easy to make it work. Just needed to be more rigorous. Thank you.
>
It would be helpful if you describe what you mean. This error message is new to
me, and appears to reflect new mechanics in the upcoming Gromacs release. If
you describe what the problem was, how you resolved it, what your pdb2gmx
command line was, and anything else that might be useful, that would likely help
others solve this issue in the future.
-Justin
> On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipooja at gmail.com
> <mailto: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
> <mailto: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>
> <mailto: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> <mailto: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>
> <mailto: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> <mailto: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 <http://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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>
> --
> 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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