Hi all!
I am in charge with the analysis of multi-chain protein where each
chain defined as separate itp file in the topology.
My task is to make new ndx file for given tpr file defining chain A as
separate ndx group and all of the rest of the protein group but not
Chain A. Assuming to select chai
Hi,
Check out out gmx select. See
http://manual.gromacs.org/documentation/5.1/user-guide/cmdline.html#selection-syntax-and-usage
Mark
On Fri, Apr 29, 2016 at 12:37 PM James Starlight
wrote:
> Hi all!
>
> I am in charge with the analysis of multi-chain protein where each
> chain defined as se
Sory I did not find here the solution to my case
2016-04-29 12:40 GMT+02:00 Mark Abraham :
> Hi,
>
> Check out out gmx select. See
> http://manual.gromacs.org/documentation/5.1/user-guide/cmdline.html#selection-syntax-and-usage
>
> Mark
>
>
>
> On Fri, Apr 29, 2016 at 12:37 PM James Starlight
> w
James,
Please try spending some time learning how to use GROMACS tools. Just
because there's a mailing list it doesn't mean that you shouldn't try
figuring things out by yourself beforehand.
This is far too basic!
1. Protein
2. Chain A
> 1 && ! 2
On 29 April 2016 at 11:44, James Starlight wro
Dear Gromacs Support,
I am writing regarding cyclic peptides simulation. I have gone through several
discussion on mailing list.
https://www.researchgate.net/post/How_to_define_energy_minimization_parameters_for_a_cyclic_peptide_GROMACS
http://permalink.gmane.org/gmane.science.biology.gromacs.u
These errors are telling you that for some of the atoms, the listed
parameter types (error warnings by grompp) are not defined in forcefield
files (eg: ffbonded.itp), Check the atoms and check your corresponding
forcefield files along with the procedure of system set up.
regards,
sarath
--
Sara
Hi,
I'm working on a protein and two cofactors and one substrate, I have too
simulate all this system on GROMACS. I'm in the first stage: choosing a force
field, box type and dimensions, water molecules...etc.
I would like to know more about the water molecule types (I looked on the
internet
you can look the following paper for the properties of different water
models.
Simulating water with rigid non-polarizable models: a general perspective
Phys. Chem. Chem. Phys., 2011, 13, 19663–19688.
In this paper they compare all the water models based on their different
thermodynamics and
dyna
On 4/29/16 9:17 AM, abhijit Kayal wrote:
you can look the following paper for the properties of different water
models.
Simulating water with rigid non-polarizable models: a general perspective
Phys. Chem. Chem. Phys., 2011, 13, 19663–19688.
In this paper they compare all the water models bas
On 4/29/16 2:50 AM, Brett wrote:
Dear All,
Here I have 2 questions related to the ligand.gro and ligand.itp preparation
for the md of protein-ligand complex.
First, we have different ways to get the ligand.itp by different serves which
use different electronic charge assignment methods. I
Dear Gromacs user,
My system is a metal surface with thousands of Water molecule on it,
normally surface(3 nm) is in the bottom of the box and the rest on top is
water(6 nm). My target is to plot "density profile" of either WATER or OW
or HW along to Z(Normal distance above solid surface); 5 ns NV
Yep, thank so much!
It has already been 5 years of the usage of Gromacs since finishing
of my PhD and still far away of understanding of all fundamentals !
James
2016-04-29 13:02 GMT+02:00 Catarina A. Carvalheda dos Santos
:
> James,
>
> Please try spending some time learning how to use GROMACS
Dear all,
Thank your for your answers.
@ Justin,
Where can I found informations related to the compatibility of one water type
with the force field that I choose for my protein? in other words "where can I
found information about the water type that had been used for the
parametrisation of
Dear All,
If prodrug server wrongly assign charge group for a ligand, then what should I
do? For example, I have a charge group of -1 group, however prodrug server
including more atoms for this charge group and make the net charge of this
charge group 0 charge.
Brett
--
Gromacs Users mailin
On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
Dear all,
Thank your for your answers.
@ Justin,
Where can I found informations related to the compatibility of one water type with the
force field that I choose for my protein? in other words "where can I found
information about the water type th
On 4/29/16 9:52 AM, Brett wrote:
Dear All,
If prodrug server wrongly assign charge group for a ligand, then what should I
do? For example, I have a charge group of -1 group, however prodrug server
including more atoms for this charge group and make the net charge of this
charge group 0 cha
Justin, as always is absolutely right. The paper that I have suggested is
just compare the different water models with the bulk properties. And the
bio molecular forcefields are compatible with particular type water
model. Like charmm force field is compatible with TIP3P water.
On Fri, Apr 29, 2
Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 )
comparing the 7 force-fields and 3 common water models (for each force-field,
except gromos) and found that at least for sampling protein behavior, TIP3P,
TIP4P, and SPC/E can all be interchanged between Charmm27, OPLS
Alexander,
For question 1.
-b 500 gives a time average density for 500ps or 0.5ns. If you change it to
5000, it'll show the time average density for 5ns and the graph will be
much smoother.
Regards,
Ashutosh Shah
On Friday, April 29, 2016, Alexander Alexander
wrote:
> Dear Gromacs user,
>
> My
Hi,
I am simulating a nucleic acid in the presence of a 15X15 single
walled carbon nanotube using CHARMM 27 force field and TIP3P water model.
In my previous published work, I did the simulation inside a cubic box and
everything ran fine but as of now whenever I am switching over to a
triclini
On 4/29/16 11:08 AM, Ashutosh Akshay Shah wrote:
Alexander,
For question 1.
-b 500 gives a time average density for 500ps or 0.5ns. If you change it to
5000, it'll show the time average density for 5ns and the graph will be
much smoother.
That's not correct. The -b option is the starting po
On 4/29/16 10:20 AM, Smith, Micholas D. wrote:
Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 )
comparing the 7 force-fields and 3 common water models (for each force-field,
except gromos) and found that at least for sampling protein behavior, TIP3P,
TIP4P, and S
On 4/29/16 11:22 AM, Alexander Alexander wrote:
Thanks for your response.
That I know, the problem is not with "-b" as it clear that with "-b 500",
the first 500 frame will be discarded from analysing.
But, I am still looking forward to hearing more from you.
RDF is explained in the manual.
@Justin,
As I recall it was the standard TIP3P, so that it could be compared across the
force-fields. The biggest difference found in this work between water models
was the number of water-protein hydrogen bonds are altered, but peptide-peptide
contacts and structure, regardless of water model,
Thanks for your response.
That I know, the problem is not with "-b" as it clear that with "-b 500",
the first 500 frame will be discarded from analysing.
But, I am still looking forward to hearing more from you.
Cheers,
Alex
On Fri, Apr 29, 2016 at 5:11 PM, Justin Lemkul wrote:
>
>
> On 4/29/1
Not really a specific publication I am comparing, but,in general I was
meaning.
Anyway,
do you know please why density profile differs a bit when "... -f case.trr
..." is used instead of "... -f case.xtc ..." in gmx density for a
simulation? Which one is preferred to use in this order?
Cheers,
Al
Dear users,
I am looking at the function vrescale_resamplekin() (in coupling.c)
that generates a new value for the kinetic energy according to
equation (7) from the original paper by Bussi et al in JCP (2007).
Maybe this is a stupid question or I am missing something, but I have
a doubt about the
Good afternoon,
I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
(Glucose-6-phosphate ) to observe how mutants affects the binding.
Following Justin tutorial (thank you Justing for providing it), I use
PRODRG to generate the topology for G6P and I then included in the prote
On 4/29/16 11:44 AM, Alexander Alexander wrote:
Not really a specific publication I am comparing, but,in general I was
meaning.
Anyway,
do you know please why density profile differs a bit when "... -f case.trr
..." is used instead of "... -f case.xtc ..." in gmx density for a
simulation? Whic
On 4/29/16 12:08 PM, Francesco Carbone wrote:
Good afternoon,
I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
(Glucose-6-phosphate ) to observe how mutants affects the binding.
Following Justin tutorial (thank you Justing for providing it), I use
PRODRG to generate the
Thank you for your reply Justin,
Of course I'll investigate the suitability of the PRODRG topology.
I was simply trying to see if I could quickly set up a simulation before
checking.
I thought that I was converting to united-atom conformation with pdb2gmx
when selecting the GROMOS ff option.
F
On 4/29/16 12:48 PM, Francesco Carbone wrote:
Thank you for your reply Justin,
Of course I'll investigate the suitability of the PRODRG topology.
I was simply trying to see if I could quickly set up a simulation before
checking.
I thought that I was converting to united-atom conformation wit
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