[gmx-users] Capping residues
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 7 22:47:33 CEST 2010
Sai Pooja wrote:
> I checked again and the error does not go. Please read the steps below.
>
> The pdb file I started off with did not have any hydrogens. However, the
> way I had specified the capping residues in the .rtp file (SEE MARK'S
> MAIL), I had to specify hydrogens in the pdb file for the capping
> residues. So I used pymol to add hydrogens to my pdb file. I then used
> this file with charmm force field. However, pymol had added hydrogens
> everywhere and this was different from the definition of the standard
> residues defined in the .rtp file. I could not directly use -ignh
> because I needed the hydrogens for the capping residues. So I created a
> file that contained the hydrogens on the capping residues only. This
> resolved the error related to hydrogens.
>
Probably an easier and more reliable approach would simply be to create an .hdb
entry for your capping groups.
>
> Error-from previous mail-NOT RESOLVED
> (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
>
Maybe this is just showing up incorrectly in my mail client, but I wonder if
that CH3 is somehow misaligned and therefore not correctly identified. I
presume that you changed the residue name in the .rtp file accordingly? I
suppose the error message would be different (something like "residue not
found") but I just want to make sure. Mark's entry used NAC.
> 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 )
>
> The error stated in the previous mail(quoted above) occurred when I
> chose "none" for the both terminals or the carboxylic terminal option
> (using -ter). It worked fine if I chose "none" at the N terminal and any
> other option except "none" at the carboxylic acid terminal.
> So I chose "none" at N terminal and some option randomly at the
> carboxylic acid terminal. As expected, it adds a terminal at that end of
> the residue before my capping residue which is something I DONT want. I
So does pdb2gmx somehow add the C-terminal cap after the carboxylate terminus?
> havent been able to find a way around it. Interestingly, when I generate
> a pdb file using -q, and open that pdb file in pymol, I dont get the
> terminal carboxylic acid that pdb2gmx gives in the .gro file.
>
So the cap is applied properly in that structure?
> I am not sure how to correct this. One way would be to remove those
> entries from the final .gro and .top file but not sure if that would be
> right.
>
This all sounds very fishy. This may be worth a bugzilla entry, but only if you
can build the structure in a very sound way, probably using .hdb entries (or an
appropriate all-atom structure, which you've yet to demonstrate).
-Justin
> Pooja
>
>
>
>
>
>
> On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> 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> <mailto: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>
> <mailto: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>>
> <mailto: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>> <mailto: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>>
> <mailto: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>> <mailto: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
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>
> -- ========================================
>
> 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> <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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>
> --
> ========================================
>
> 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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--
========================================
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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