[gmx-users] Capping residues
Sai Pooja
saipooja at gmail.com
Thu Jul 8 00:32:09 CEST 2010
This probably is my ignorance but the error and the "bug" goes when I
replaced CBX with NAC everywhere.
On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>>
>>
>> -- ========================================
>>
>> 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.
>>
>
> --
> ========================================
>
> 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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