[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
maria goranovic
mariagoranovic at gmail.com
Thu Jan 20 23:28:36 CET 2011
Gee. My mistake then. I did not realize the difference between -COO and
Zwitterion_COO-.
However, when I use the zwitterion termini on both ends of the other chain,
the total charge is 4.010, which is also *slightly*´ disturbing. I have seen
numbers like 2.999999, which are still better. Is 4.010 acceptable within
rounding off errors?
thank you for helping
-Maria
On Thu, Jan 20, 2011 at 2:00 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> maria goranovic wrote:
>
>> I did use -ter and chose -COO and NH3+. Am i supposed to chose
>> Zwitterion_COO- and Zwitterion_NH3+ ?
>>
>
> That's what I said, and that's what you have, isn't it? A single amino
> acid that should have both its termini charged?
>
> -Justin
>
> On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> maria goranovic wrote:
>>
>> Hi
>>
>> I have figured out the vacuum slow problem. It turns out I was
>> using PBC in vacuum with PME. It is now fixed.
>>
>> The other problem is still there. My protein has 2 chains. one
>> chain is simply a glutamate residue. Its charge (both terminii
>> charged is -1.11 instead of -1). here is the section of the
>> topology with the charges. Why does pdb2gmx assign a charge of
>> -1.11 instead of -1 if there is a free glutamate molecule with
>> NH3+ and COO- at the terminii ?
>>
>>
>> You're not choosing the termini correctly. Use -ter with pdb2gmx
>> and select the zwitterion forms of both termini.
>>
>> -Justin
>>
>>
>> 1 opls_287 484 GLU N 1 -0.3
>> 14.0067 ; qtot -0.3
>> 2 opls_290 484 GLU H1 1 0.33
>> 1.008 ; qtot 0.03
>> 3 opls_290 484 GLU H2 1 0.33
>> 1.008 ; qtot 0.36
>> 4 opls_290 484 GLU H3 1 0.33
>> 1.008 ; qtot 0.69
>> 5 opls_283 484 GLU CA 1 0.04
>> 12.011 ; qtot 0.73
>> 6 opls_140 484 GLU HA 1 0.06
>> 1.008 ; qtot 0.79
>> 7 opls_136 484 GLU CB 2 -0.12
>> 12.011 ; qtot 0.67
>> 8 opls_140 484 GLU HB1 2 0.06
>> 1.008 ; qtot 0.73
>> 9 opls_140 484 GLU HB2 2 0.06
>> 1.008 ; qtot 0.79
>> 10 opls_274 484 GLU CG 3 -0.22
>> 12.011 ; qtot 0.57
>> 11 opls_140 484 GLU HG1 3 0.06
>> 1.008 ; qtot 0.63
>> 12 opls_140 484 GLU HG2 3 0.06
>> 1.008 ; qtot 0.69
>> 13 opls_271 484 GLU CD 4 0.7
>> 12.011 ; qtot 1.39
>> 14 opls_272 484 GLU OE1 4 -0.8
>> 15.9994 ; qtot 0.59
>> 15 opls_272 484 GLU OE2 4 -0.8
>> 15.9994 ; qtot -0.21
>> 16 opls_271 484 GLU C 5 0.7
>> 12.011 ; qtot 0.49
>> 17 opls_272 484 GLU O1 5 -0.8
>> 15.9994 ; qtot -0.31
>> 18 opls_272 484 GLU O2 5 -0.8
>> 15.9994 ; qtot -1.11
>>
>>
>>
>> On Thu, Jan 20, 2011 at 11:55 AM, 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:
>>
>>
>>
>> On 01/20/11, *maria goranovic * <mariagoranovic at gmail.com
>> <mailto:mariagoranovic at gmail.com>
>> <mailto:mariagoranovic at gmail.com
>>
>> <mailto:mariagoranovic at gmail.com>>> wrote:
>>
>> Hi
>>
>> I have a protein whose topology I built using pdb2gmx
>> with the -ss
>> option and the opls-aa force field. When I run grompp,
>> the total
>> charge on the protein is reported as 2.9 (not 2.999). Why a
>> non-zero charge? Does this have something to do with the
>> disulfide
>> bridge?
>>
>>
>> Something is materially wrong, like mangled termini. Have a
>> look at
>> the resulting structure.
>>
>>
>> Secondly, when I run a simulation of the same protein
>> (7000 atoms)
>> with certain restraints in vacuum, the simulation runs
>> very slow.
>> I am wondering why. I am not using particle
>> decomposition. the box
>> size is 50 x 50 x 50 nm. Using 4.5.3
>>
>>
>> Have a look at the end of the .log file for some performance
>> data.
>> How are you assessing "very slow"?
>>
>> Mark
>> --
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>>
>>
>> -- Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
>> -- ========================================
>>
>> 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
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>> Please search the archive at
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>>
>>
>>
>>
>> --
>> Maria G.
>> Technical University of Denmark
>> Copenhagen
>>
>>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>
--
Maria G.
Technical University of Denmark
Copenhagen
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