On Sun, Nov 14, 2010 at 14:50, leila karami wrote:
> I made a selection.dat file as follows:
>
> waterO = group SOL and name OW;
> heavy1 = group Protein_A and group "Protein-H";
> heavy2 = group Protein_B and group "Protein-H";
> inter = waterO and within 0.35 of heavy1 and within 0.35 of heavy2;
Dear gromacs users
I was trying to count waters involved in the interface between Protein_A and
Protein_B.
I made a selection.dat file as follows:
waterO = group SOL and name OW;
heavy1 = group Protein_A and group "Protein-H";
heavy2 = group Protein_B and group "Protein-H";
inter = waterO and wi
On 14/11/2010 7:57 PM, leila karami wrote:
Dear Mark
I have a question as same as atila petrosian, but my system is
protein-dna.
you said [IIRC g_select has some better documentation available once
you run it and ask for help, somewhat like make_ndx].
please explain IIRC more. Is IIRC a pr
Dear Mark
I have a question as same as atila petrosian, but my system is protein-dna.
you said [IIRC g_select has some better documentation available once you run
it and ask for help, somewhat like make_ndx].
please explain IIRC more. Is IIRC a program or a list of archives?
any help will highl
On 14/11/2010 12:21 AM, atila petrosian wrote:
Dear Mark and gromacs users
thanks for your time and attention.
how to make selection.dat file? what should be in that?
please clarify this new tool more. how can I obtain what I need
(number of water molecules (interfacial) to be within
2.4 A
Dear Justin
I used g_dist -f .xtc -s .tpr -n .ndx -o -lt -dist 1
but program give me only lifetime.xvg. there are no dist.xvg file. why?
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atila petrosian wrote:
Dear Justin
are you sure g_dist -dist give me what I need. if so, how?
since, dist.xvg gives distance vs time and lifetime.xvg gives number of
contact vs time. while, I want number of water molecules (interfacial)
to be within 2.4 A distance from both the protein and
Dear Justin
are you sure g_dist -dist give me what I need. if so, how?
since, dist.xvg gives distance vs time and lifetime.xvg gives number of
contact vs time. while, I want number of water molecules (interfacial) to be
within 2.4 A distance from both the protein and the ligand during
simulation.
atila petrosian wrote:
Dear Mark and gromacs users
thanks for your time and attention.
how to make selection.dat file? what should be in that?
please clarify this new tool more. how can I obtain what I need (number
of water molecules (interfacial) to be within
2.4 A distance from both the
Dear Mark and gromacs users
thanks for your time and attention.
how to make selection.dat file? what should be in that?
please clarify this new tool more. how can I obtain what I need (number of
water molecules (interfacial) to be within
2.4 A distance from both the protein and the ligand durin
On 13/11/2010 9:12 PM, atila petrosian wrote:
Dear all
my system includes protein, ligand and water.
I want to obtain number of water molecules (interfacial) to be within
2.4 A distance from both the protein and the ligand during simulation.
also, exact numeration of each water being in inter
Dear all
my system includes protein, ligand and water.
I want to obtain number of water molecules (interfacial) to be within 2.4 A
distance from both the protein and the ligand during simulation. also, exact
numeration of each water being in interface between protein and ligand.
--
gmx-users m
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