[gmx-users] Solvating protein

[Justin A. Lemkul]

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>> 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.
> 
> 
>     -- 
>     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/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/mailing_lists/users.php
> 
> 
> 
> 
> -- 
> 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

========================================