[gmx-users] Solvating protein
Justin A. Lemkul
jalemkul at vt.edu
Fri Jul 9 19:36:04 CEST 2010
Sai Pooja wrote:
> Now I use genion and it says no ions to add?
>
> Using a coulomb cut-off of 1 nm
> No ions to add and no potential to calculate.
>
> command used: genion -s ions.tpr -neutral -pname NA+ -nname -CL- -o
> solions.gro -p finalnoss.top
>
You haven't told genion to add anything. Use -np and/or -nn as appropriate.
-Justin
>
> On Fri, Jul 9, 2010 at 1:26 PM, Sai Pooja <saipooja at gmail.com
> <mailto:saipooja at gmail.com>> wrote:
>
> I checked topology file but going with grompp makes sense. Thank you.
>
>
> On Fri, Jul 9, 2010 at 1:11 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Sai Pooja wrote:
>
> Well thats the thing. I have checked my pdb files. All
> residues have
>
>
> There aren't charges in a .pdb file, unless you've somehow added
> them into one of the fields yourself. The file you need to
> check is your topology. A running value of the net charges is
> given in the [atoms] directive. Charges are assigned by pdb2gmx
> based on what is expected in the .rtp file and what you chose to
> assign in terms of protonation state.
>
>
> either 0 or integer net charges. The number 0.9999994 seems
> like a rounding off error especially since the output of
> genbox says that the system has zero net charge. Again, I
> encounter this no-zero net charge
>
>
> genbox reads coordinate files, so I don't know how any charge it
> prints is meaningful. It tells me there is a zero charge on a
> lysozyme system that I know has a +8 charge (regardless of
> whether or not I pass it a topology as well), so don't believe
> genbox. Believe grompp. The magnitude is indeed due to small
> rounding errors. It should be interpreted as -1.
>
> -Justin
>
> when I run grompp with an mdp file for energy minimization
> with the protein( excluding hydrogen ) restrained.
>
> I am using the charmm implemented version of gromacs.
>
> Pooja
> On Fri, Jul 9, 2010 at 11:49 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 10/07/2010 1:28 AM, Sai Pooja wrote:
>
>
> Hi,
>
> When I start from a energy minimized protein in
> vacuum and
> solvate it using genbox, the output message says that the
> protein has zero charge. So I skip the genion step. I
> follow
> this with energy minimization of the solvated protein
> followed
> by restraining the protein and then doing a short
> mdrun (as is
> the usual procedure outlined in most tutorials).
> However, when I
> run the grompp command as the first step for the position
> restrained md, it runs but prints a note saying that
> the system
> has non-zero charge ~ - 0.9999.
>
> NOTE 2 [file finalnoss.top, line 8070]:
> System has non-zero total charge: -9.999994e-01
>
> I dont understand. Do I need to run the genion step
> anyway or is
> it okay to continue with this system?
>
>
> I'd believe grompp before genbox. Surely you know already
> what is in
> your system, and thus its total charge. You should
> already know the
> protonation state of all of your relevant protein
> residues, because
> you made choices for them with pdb2gmx.
>
> Mark
>
>
>
> Pooja
>
> -- Quaerendo Invenietis-Seek and you shall
> discover.
>
>
>
> -- Quaerendo Invenietis-Seek and you shall
> discover.
>
>
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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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