Dear Gromacs Users,
I have GPCR-protein complex simulation and want to calculate buried surface
area of the complex. I am using gmx sasa but facing problem in using the
command especially the -output part.
I need to calculate SASA for unbound receptor,unbound ligand and of
complex. I have made i
Hi,
My system contains, nanotube with amino acids in aqueous solution. I want
to know how amino amicds cover nanotube surface after adsorption. Can i do
it by gmx sasa? It seems this tool just calculate (solution relavent
properties)coverage?
Best
Rose
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Dear All,
I am using 'gmx_mpi sasa' module as below:
gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 5
Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein.
Dear All,
I am using 'gmx_mpi sasa' module as below:
gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 5
Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein.
On 8/9/17 10:00 PM, Mohammad Zahidul Hossain Khan wrote:
Dear Sir
Does anyone know how to measure the SASA energy with unit (kj/mol or
kcal/mol)
when i give this command:
*gmx sasa -f b.trr -s b.tpr -o b.xvg*
I got in Y-axix "Area (nm\S2\N)"
and when I give this command
*gmx sasa -f b.trr -s
Dear Sir
Does anyone know how to measure the SASA energy with unit (kj/mol or
kcal/mol)
when i give this command:
*gmx sasa -f b.trr -s b.tpr -o b.xvg*
I got in Y-axix "Area (nm\S2\N)"
and when I give this command
*gmx sasa -f b.trr -s b.tpr -odg b.xvg*
I got in Y axix "D Gsolv"
but I do not kno
On 2/23/16 9:45 AM, Sara Del Galdo wrote:
Hi Gromacs users,
I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and wh
Hi Gromacs users,
I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and which of the two tool is more reliable?
Thanks i
On 1/31/16 2:24 PM, Eric Smoll wrote:
Hello Gromacs Users,
"gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii
are obtained from the following reference:
"A. Bondi, van der Waals Volumes and Radii, J.
Phys. Chem. 68 (1964) pp. 441-451"
Can the user still control the rad
Hello Gromacs Users,
"gmx sasa" in Gromacs 5.0.6 returns a message stating that all atom radii
are obtained from the following reference:
"A. Bondi, van der Waals Volumes and Radii, J.
Phys. Chem. 68 (1964) pp. 441-451"
Can the user still control the radii used by editing a local copy of the
sha
That was also part of the bug fix: with the fixed version, you should get
the same number of rows and the same areas on each row, but the first
column will have the correct residue numbers.
Teemu
On Thu, Nov 5, 2015, 19:12 Francesco Carbone wrote:
> Thank you for your reply,
> Everything makes
Thank you for your reply,
Everything makes sens, the only thing that I still haven't understood is
the reason for which I have multiple lines for the residues.
Are those atoms? then why are there, if I want the single residue?
Regards,
Fra
On 5 November 2015 at 16:33, Teemu Murtola wrote:
> Hi
Hi,
The issue with incorrect legends and X axis has been fixed in 5.0.6.
As for the four columns, you are asking gmx sasa to calculate the same
numbers twice, so you get them twice: according to gmx sasa -h, the area of
-surface selection is always calculated, and -output (which is optional)
just
Good afternoon,
I calculated the residue area (-or) over my trajectory, but I have trouble
understanding the output.
With gromacs 4.6 I obtain a clean file:
residue value standard dev
27 4.654781.19505
280.990566 0.966795
29 1.77202 0.6297
The other possibility is that your index groups do not have the atom
indices in an increasing order. If this is the case, just sort the atoms,
or don't use make_ndx as an intermediate step.
Teemu
On Fri, Sep 4, 2015, 14:20 Francesco Carbone wrote:
> thank you for the reply, but the residues are
thank you for the reply, but the residues are in the same protein.
I simply select a list of residues that interact with the substrate.
(echo "r 171 263 201 202 205 395 365 239 360 258"; echo "name 10 G6P"; echo
"q") | make_ndx -f $nameprod.gro -o $name1.ndx
residues 171 263 201 202 205 395 365 2
thank you for the reply, but the residues are in the same protein.
I simply select a list of residues that interact with the substrate.
(echo "r 171 263 201 202 205 395 365 239 360 258"; echo "name 10 G6P"; echo
"q") | make_ndx -f $nameprod.gro -o $name1.ndx
residues 171 263 201 202 205 395 365 2
Hello,
On Fri, Sep 4, 2015 at 1:51 PM Francesco Carbone
wrote:
> I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
> recognise non-standard groups for the -output flag.
> I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer )
> and every time I specify
Good morning,
I've recently started using gromacs 5.0.4 and I can't make"gmx sasa" to
recognise non-standard groups for the -output flag.
I have three groups (G6P, Co-enzyme and strNADP+; all subset of the dimer )
and every time I specify one of the three with "-output" flag I get:
"Inconsistency i
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