On Fri, 13 Jun 2008 02:46:16 +0530 (IST)
[EMAIL PROTECTED] wrote:
Dear Tsjerk,
Actually, I have defined the groups for Temp-coupling as:
tc-grps = Protein_CA2+ SOL
Thus, I felt would I be incorporating any errors, if I define my
energygrps as:
energygrps = Protein SOL
I have generated my index.ndx file exactly the way you defined
(Protein_CA2+) and supplied it to the grompp.
"energygrps" ONLY defines groups for which the energies will be
stored in the output (ener.edr) for you to access them easily
with g_energy.
The definition of energygrps will in no manner affect the way the
interaction energies are calculated in the propagation of the
program, when you run mdrun. They are actually not used, forces
are.
XAvier
Thanks for your valuable time.
Regards,
Tuhin
Hi Tuhin,
It depends on what you do. In both cases you will have to run grompp
with an index file with a group specified, containing both the Protein
and the calcium ion. You can take an existing index file (created
simply with "echo q | make_ndx -f mystructure.gro") and add the number
of the calcium ion under the label [ Protein ] or you make the
combination within make_ndx, combining the two groups. In the later
caseyou're likely to end up with a group called Protein_CA2+. Key
issue to understand is that it's not sufficient to only define a group
in the .mdp file. Except for the standard groups gromacs knows, a
group will have to be defined through an index file.
Cheers,
Tsjerk
On Thu, Jun 12, 2008 at 10:08 PM, <[EMAIL PROTECTED]> wrote:
Dear Mark,
To continue further, do I need to define my "energy groups" as:
energygrps = Protein_CA2+ SOL
OR, I could do as:
energygrps = Protein SOL
Best,
Tuhin
[EMAIL PROTECTED] wrote:
Dear Gromacs users,
My protein is a heterodimer (a small chain:A and a large chain:B). A
single Ca2+ ion is found interacting with residues from chain:B only.
In
the .pdb file the Ca2+ is assigned a chain:B identifier.
HETATM 6504 CA CA B1579 23.021 -16.233 6.204 1.00 7.96
CA
When I visualize the protein and generate a conolly surface, I could
see
the Ca2+ ion completely buried within chain:B. Now, I have two
questions:
1. I would like to perform an MD on the above protein using Gromacs
3.2.1
Unless you have a really good reason (e.g. compatibility with old
results), you should be planning to use a more recent version.
suit with ffG43a1 forcefield. I know the Ca2+ ion is not accessible to
solvent molecules. Will the forcefield parameter for Ca2+ sufficient
enough to take this fact into account. I mean, Ca2+ in solvent and Ca2+
in
protein; for both the cases could I use the Ca2+ with +2 charge ? What
about the vdw contribution between the interacting residues from
chain:B
and Ca2+ ion ?
To answer that, you should read about how these parameters were
developed for the force field. Perhaps you will need to refine them
yourself - but this is not a good thing to do early in your MD and/or
GROMACS experience.
2. When defining groups for Temp-coupling; could I do something like
(as
I
know the Ca2+ not accessible to solvent):
tc-grps = Protein_CA2+ SOL
That would be reasonable and effective.
Mark
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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