[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
>         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> <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.
> 
> 
> 
> 
>         -- 
>         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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-- 
========================================

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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