[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 20 14:00:52 CET 2011
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
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto: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 or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
>
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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>
> 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 or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list