[gmx-users] Capping residues
Sai Pooja
saipooja at gmail.com
Wed Jul 7 22:29:03 CEST 2010
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.
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
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 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.
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.
Pooja
On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <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>> 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.
>>
>>
>>
>>
>> --
>> 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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