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.abra...@anu.edu.au
<mailto:mark.abra...@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
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========================================
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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