I came across a tool for making "porcupine" plots out of my PCA
analysis, but first I need to perform the analysis with a program that
accepts .cdr (amber traj) file format (the name of the program is
PCAZIP). I would like to know if there is a way to convert my .trr
trajectories into these .cdr on
Hi can I obtain the mean number of hydrogen bonds plus an error
estimate from the hbnum.xvg. I have tried using g_analyze for this,
but the values I got for the mean are not as near as what I would have
expected. Could it be that g_analyze is reading the wrong column. If
that is the case, what woul
Once I have the eigenvalue.xvg, how do I calculate the fraction of
total RMSF that each eigenvector contributes, i.e., how do I find out
that, for example, my first eigenvector is responsible for 73% of my
total rmsf and so on.
Thank you in advance
Fabrício Bracht
__
I have created an mdp file with 202 groups for monitoring in the
energygrps string. Being 201 of these aminoacids which interact with
the 202nd which is the ligand. The problem is that I found out that
this does not work properly, and also does not work the way I thought
it would work. Well, the de
t;
> This should give you as output all the pair interacts and you can
> select the ones you want ... ?!
>
> On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:
>
>> I have created an mdp file with 202 groups for monitoring in the
>> energygrps string. Being 201 of these a
>This should give you as output all the pair interacts and you can
>select the ones you want ... ?!
>
>On Jul 17, 2009, at 4:23 PM, Ragnarok sdf wrote:
>
>> I have created an mdp file with 202 groups for monitoring in the
>>energygrps string. Being 201 of these aminoacid
I am performing FEP do obtain the dimerization of a protein in
membrane. The lambda intervals i am using are 0.05 for each window.
After that I rerun each lambda .trr perturbing the system (plus)0.05
and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG
for each delta lambda.
Well, I
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>> I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I rerun each lambda .trr perturbing the syste
7, 2009 at 2:35 AM, Carsten Kutzner wrote:
>
>> On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote:
>>
>> I am performing FEP do obtain the dimerization of a protein in
>>> membrane. The lambda intervals i am using are 0.05 for each window.
>>> After that I reru
on. The soft core potential is constructed so that
> the end points at lambda=0 and 1 represent the 'native' states (with no
> influence from the soft core parameters), and that intermediate values
> produce a smooth transformation.
> Best,
>
> Floris
>
>
> __
core potential is constructed so that
> the end points at lambda=0 and 1 represent the 'native' states (with no
> influence from the soft core parameters), and that intermediate values
> produce a smooth transformation.
> Best,
>
> Floris
>
>
>
I am working with a membrane protein dimer, each monomer being
constituted of a single helix. I have already studied the effect of
point mutations on the structure and the free energy involved by using
FEP. But I have read a paper in which the author has done PMF
calculations in order to calculate
I am trying to learn how to use the pull code to separate a dimer. I have
read gromacs 4 manual and a tutorial I found on CSC, but it seems I still
haven´t got the knack.
My system is consisted of a dimer inserted into a membrane lipid bilayer. I
have included the following lines into my mdp parame
= r_1-30
pull_group1 = r_31-60
pull_vec1 = 1 1 0
pull_init1 = 0.0
pull_rate1 = 0.05
pull_k1 = 30
pull_constr_tol = 1e-06
pull_pbcatom0 = 0
pull_pbcatom1 = 0
Fabrício Bracht
>
> Ragnarok sdf wrote:
> > I am trying to learn how to use the pull code to separate a dimer. I
> > ha
somekind of standard, or would I
need to rely on certain parameters, like rmsf of my protein or area per
lipid?
Fabrício Bracht
>
> Ragnarok sdf wrote:
> > Hi Justin, yes the intention is to pull the dimer apart within the
> > plane of the bilayer. I've ran a few mo
somekind of standard, or would I
need to rely on certain parameters, like rmsf of my protein or area per
lipid?
Ps: Sorry for the re-sending, I forgot to edit my subject box.
Fabrício Bracht
>
> Ragnarok sdf wrote:
> > Hi Justin, yes the intention is to pull the dimer apar
istance. But this is not convenient if you want to run
> multiple
> simulations simultaneously.
> In both methods checking the convergence of the re/constraint force is
> critical.
>
> Berk
> >
> > Ragnarok sdf wrote:
> > > Hi Justin, yes the intention is to
I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC from
tieleman's website as a starting structure. I've run a short 1 ns
semi-isotropic simulation at 323 K and monitored the area per lipid as a
stability parameter for my membrane simulation. If the area per lipid
maintains the sa
When analysing FEP simulations. After running g_energy -f fep000.edr -f2
fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I tried
to obtain the standard deviation for this ensemble average using g_analyze
-f runavg.xvg, but I've noticed that the average values are quite different
Is there a correct way to obtain the standard deviation for these data sets?
>
> Ragnarok sdf wrote:
> > When analysing FEP simulations. After running g_energy -f fep000.edr -f2
> > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I
> tried
> >
Is there a correct way to obtain the standard deviation for these data sets?
> >
> > Ragnarok sdf wrote:
> > > When analysing FEP simulations. After running g_energy -f fep000.edr
> -f2
> > > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT
mate?
>
> Berk
>
> Date: Fri, 28 Aug 2009 09:30:37 -0300
> From: fabrac...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_energy and g_analyze give different averages
>
> Is there a correct way to obtain the standard deviation for these data
> sets?
&g
mate?
>
> Berk
>
> Date: Fri, 28 Aug 2009 09:30:37 -0300
> From: fabrac...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_energy and g_analyze give different averages
>
>
> Is there a correct way to obtain the standard deviation for these data
> s
I have finished a simulation using the pull code, but found nothing in the
manual or discussion list (regarding Gromacs 4) on how to create the generic
data files used as input for g_wham. I have only the two .xvg files from -pf
and -px generated from mdrun.
Another question is about what would be
Hi
I am trying to calculate the PMF by pulling two membrane protein monomers
apart using the pull code with umbrella sampling. While trying to generate
my reaction path, no matter how slow I pull, my helix starts bending (not
really bending, but it kind of tends to transform into a "C" shape inside
not appear?
Thank you
Fabrício Bracht
> On Sep 5, 2009, at 7:42 AM, Ragnarok sdf wrote:
>
> > Hi
> > I am trying to calculate the PMF by pulling two membrane protein
> > monomers apart using the pull code with umbrella sampling. While
> > trying to generate my reaction
I have done FEP simulations and am trying to find a way to report the error
related to the values of relative delta G found. I have simulated 20 windows
each with an interval of lambda of 0.05. Then used -rerun option from mdrun
to perform the same simulation with a lambda value of (lambda+0.05) an
I have done FEP simulations and am trying to find a way to report the error
related to the values of relative delta G found. I have simulated 20 windows
each with an interval of lambda of 0.05. Then used -rerun option from mdrun
to perform the same simulation with a lambda value of (lambda+0.05) an
While trying to analyse my several windows with g_wham the following error
appears :
Fatal error:
Pull geometry direction not supported
my entry files consist on the several px.xvg listed in a .dat entry file and
the several .tpr from each of the simulations also listed in a tpr.dat file_
>
>
> Ragnarok sdf wrote:
> > While trying to analyse my several windows with g_wham the following
> error
> > appears :
> >
> > Fatal error:
> > Pull geometry direction not supported
> >
> > my entry files consist on the several px.xvg liste
>
>
>
> Ragnarok sdf wrote:
> >
> > Ragnarok sdf wrote:
> > > While trying to analyse my several windows with g_wham the
> > following error
> > > appears :
> > >
> > > Fatal error:
> > >
>
> >
> > Ragnarok sdf wrote:
> > > While trying to analyse my several windows with g_wham the
> > following error
> > > appears :
> > >
> > > Fatal error:
> > > Pull geometry direction not sup
>
> Ragnarok sdf wrote:
> >
> > Ragnarok sdf wrote:
> > > While trying to analyse my several windows with g_wham the
> > following error
> > > appears :
> > >
> > > Fatal error:
> > > Pull
I have performed FEP calculations by averaging backward and forward
perturbations in intervals of 0.05 regarding lambda. The averages between
each of these sets of perturbations were summed to obtain the final free
energy with respect to that particular mutation. I have tryed to obtain the
error es
Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
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Please search the archive at http://www.gromacs.org/search before posting!
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>
> Ragnarok sdf wrote:
> > Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
>
> Units are described in section 2.2 of the manual. For g_energy, the
> units will obviously depend on the quantity involved.
>
> Mark
>
> Well, that is the reason of my questio
I am performing PMF calculations for my helix dimer using umbrella potential
and WHAM analysis. I have already obtained the main reaction coordinates and
have divided my path into several windows. From each of this windows,
corresponding to a specified distance between my two dimers, I am simulatin
>
>
>
> > To generate each window I use "trjconv -f
> > original_separation_trajectory.xtc -s topol.tpr -dump
> > time_where_specific_distance_is_found -o
> > frame_where_separation_between_structures_is_x.gro"
> > Once I have the coordinate files regarding this specific distance
> > between my pul
I would like to know if there is a way to monitor the hydrophobic
interactions between protein and any other ligand, or even within protein
protein complexes? To know which residues participate and so on.
Thank you in advance
Fabrício Bracht
___
gmx-users
I am trying to setup a simulation with a ligand and a protein using
ffamber99 forcefield. I have already generated the ligand's topology file
using acpypi and everything seems to be all right in the files generated.
However, while following the steps in the drug enzyme tutorial provided in
the grom
I am working with a protein-ligand complex in gromacs with ffamber99
forcefield. I was able to generate the topology file for my ligand with
acpypi. Was also able to insert the ligand coordinates into my protein's
coordinate file. Was also able to generate the water box with genbox. The
number of m
Hello, I was asked to post my ligand.itp file here, but apparently the file
is too big to be posted. I was supposed to receive a message telling me if
the post was accepted or not. I understand that the administrators must be
busy most of the time, so I would like to know if there is any other
poss
Well, right after I tried to post I received a message saying that my
previous message bounced because I had exceeded the size limit of 50k.
I will try to post the file again, in case the same thing happens again I
will try to attach the file.
Thank you
How large is the file? Most topology files
Hello. I will try now to send part of my itp file and if another part
of the file is needed I will send it if requested.
Below are the emails that were already sent regarding my problem.
I hope I have not caused any incovenience.
Fabrício Bracht
" I am working with a protein-ligand complex in grom
I am working with a system using ffamber99 forcefield and trying to
set up a ligand protein complex system. I have encountered some
problems with grompp now.
In my past email, the problem was that : > Fatal error: Found a second
defaults directive, file "ligand.itp", line 5. Then the following
solu
I am trying to set up a system with a helix in a decane box. I am
using dec50.gro and decane.itp files to build the box. I've used
GROMOS96 53a6 forcefield and when I run grompp the following error
comes out.
ERROR 0 [file "vegfr2.top", line 37]:
atom C10 (Res C10-107) has mass 0
-
Hello, I would like to know if there is any recommendation onto
setting up a system with a protein in a apolar solvent box. If there
is any tutorial or web page with topologies for solvents. I read that
the decane box that comes with gromacs is not to be used for
simulations, if that is true, then
I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were carried out using ffgmx fo
Hello, I was following the steps in Justin Lemkul's tutorial for
insertion of a protein in a lipid bilayer and have come accross a
problem right after using inflategro's script from Tieleman's website.
It says there that I should run an energy minimization and then
continue with the steps of the tu
Hello. I am trying to access the videos from EMBO course available in
Gromacs' wiki but I can't have access to any of them. Are they
available only for a strict community or something like that?
I also would like some advice on how to perform a calculation of
free-energy of dimerization between two
Hi, I am running a simulation of a protein DNA complex, and for this i
am using AMBER99 forcefield. The problem is that every complex I need
to run, I have to rename several residues and atoms, especially
hydrogen atoms one by one (well, actually using replace tool). And
this takes hours to get don
Hello, I've searched the archives in search of an answer for my problem and
was able to solve only part of the problem.
I am working with a DNA/Protein system with AMBER99 forcefield.
The first problem is
"...Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions:
Hello. Ie been trying to run a DNA simulation with gromacs using amber99
force field. I've started with my DNA sequence complexed with the protein,
but then decided to separate them to know exactly what the problem was. Now
I am not even using the DNA sequence from my pdb file. I`ve used the NAB
se
>
> Ragnarok sdf wrote:
> > Hello. Ie been trying to run a DNA simulation with gromacs using amber99
> > force field. I've started with my DNA sequence complexed with the
> > protein, but then decided to separate them to know exactly what the
> > problem w
integer charge.
System has non-zero total charge: -2.151740e+01
Thank you again and sorry for the delay
>
>
>
> Ragnarok sdf wrote:
>
> > Tahnk you Justein for the reply.
> > I read again chapter 5, this time I tried to be more thorough, but still
> > I don't re
Hello Justin. You asked about adding solvents or ions. Well I added solvent
to the box using genbox, but the non integer total charge comes from the
beggining of the proccess, directly from pdb2gmx. Ions didn't have the
chance to get to that part, since my grompp command gives out error about
bond
Hello Justin. I know I just sent you an email in reply to your last one, but
now things seemed to have finally worked out. What I did was simply to add a
Cytidine residue to the 5' end and a Guanine to the 3' end of each chain.
Now all of a sudden I have integer charge and everything seems to work
Hi Justin, well, actually the problem is not only with grompp, since
my non integer charges come all the way since pdb2gmx
I used as I told:
pdb2gmx -f 1vkxdna.pdb -o 1vkxdna.gro -p 1vkxdna.top
editconf -f 1vkxdna.gro -o 1vkxdna_caixa.gro -c -d 0.9 -princ
genbox -cs -cp 1vkxdna_caixa.gro -o 1vkxdna
I've been trying to install gromacs with parallel support. I've installed
the lammpi package, than fftw 3.1.2 libraries. Lamboot seems to work fine,
but when i type
# ./configure --enable-mpi
the following error appears
checking for mpxlc... no
checking for mpicc... no
checking for mpcc... no
chec
Hello,
I have ran a simulation with gromac but can't seem to be able to extract a
single structure of a determined frame from my .trr file. I wish to obtain a
pdb file good for reading in CHIMERA, for example.
I tryed the following command:
trjconv -f sim.trr -s trjtop.tpr -o pdbiwant.pdb -b 1
your error.
> Have you done any fitting and pbc related stuff or did you
> shuffle/sort your system prior to running?
>
> Cheers,
>
> Tsjerk
>
> On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <[EMAIL PROTECTED]> wrote:
> > Hello,
> > I have ran a simulation
How do I create topology files for a ligand when using ffamber99 in gromacs?
Thank you
Fabrício Bracht
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