dear gromacs users,
my protein has a cofactor FAD, and NAG sugar along with it. these are present
in the protein's PDB file itself.
while creating the topology, are we supposed to add FAD's and NAG's itp under
"Include forcefield parameters" by downloading it separately and also should I
add the
P.R.Anand Narayanan wrote:
dear gromacs users,
my protein has a cofactor FAD, and NAG sugar along with it. these are
present in the protein's PDB file itself.
while creating the topology, are we supposed to add FAD's and NAG's itp
under
"Include forcefield parameters" by downloading it separa
Hi,
What are the units of RMSD (nm or ang) in which g_rms calculates the RMSD
between two structures ?
Regards,
Nikhl
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nikhil damle wrote:
Hi,
What are the units of RMSD (nm or ang) in which g_rms calculates the
RMSD between two structures ?
The header of the .xvg file (y-axis legend) tells you the units. All units and
conventions are explained in Chapter 2 of the manual.
-Justin
Regards,
Nikhl
Send
Thanks a lot for the help.
Regards,
Nikhil
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Monday, 13 July, 2009 5:22:06 PM
Subject: Re: [gmx-users] query regarding g_rms
nikhil damle wrote:
> Hi,
> What are the units of RMSD (nm or ang)
Hi,
This question has been asked several times before on this list.
The proper way to handle this in Gromacs is to introduce two dummy mass
particles
in such a way the total mass and the moment of inertia is identical to CO2.
Then you can construct the positions of the three mass-less C and O at
Dear all,
I have did a simulation with explict water model using Gromacs-3.3.3.
To save the hard disk space, I didn't collect the coordinates of water by
using the following parameters:
dt = 0.002 ; ps !
nsteps = 3000 ; total time.
nstcomm
Hi Dechang Li,
If your simulations are different, the results will be different. It's chaos!
Cheers,
Tsjerk
2009/7/13 Dechang Li :
> Dear all,
>
> I have did a simulation with explict water model using Gromacs-3.3.3.
> To save the hard disk space, I didn't collect the coordinates of wate
Hello,
I would appreciate if someone could help with advice regarding including
the effects of an extra LJ repulsive term in Gromacs. Would this be
possible to do this without actually altering the functional form?
The extra repulsive term is applied to one single type of atom pairs. I
thought of
That may seem ridiculous, but I'm also using a *.gro file and whenever
GROMACS tells me: "File input/output error:", it means that I've not cd to
the folder in which that *.gro file exists!
On Mon, Jul 13, 2009 at 6:59 AM, Justin A. Lemkul wrote:
>
>
> mohit kumar wrote:
>
>> ok.thanx very much
Hi,
I have a doubt regarding binning technique to generate density profile and
streaming velocity. I followed Allen and Tildesley and use the following
formulae to calculate density and velocity profiles. (Consider monoatomic
species)
1) No. density of atoms in a bin 'i' = Total no. of atoms in bi
Dear all
I have since found the problem. For some reason gen-pairs = yes option
is not working, so my 1-4 interactions were being completely excluded
and not scaled by 0.5 as they should have been. Defining all 1-4 pairs
in a [ pairs ] section in conjunction with nexcl =3 in the topology
solved th
Hi Mark,
I used editconf on my .gro file with zero space between my solvent and
the box and the resulting box had the exact same dimension as the
initial box. I also performed a number of simulation runs with different
mdp parameters hoping this would provide me some indication of the cause
of the
darre...@ece.ubc.ca wrote:
Hi Mark,
I used editconf on my .gro file with zero space between my solvent and
the box and the resulting box had the exact same dimension as the
initial box. I also performed a number of simulation runs with different
mdp parameters hoping this would provide me some in
darre...@ece.ubc.ca wrote:
Hi Mark,
I used editconf on my .gro file with zero space between my solvent and
the box and the resulting box had the exact same dimension as the
initial box. I also performed a number of simulation runs with different
If you're using editconf to define zero space,
HI.
I have compiled and installed gromacs 4.0.5 on a mac running 10.5. I
have also installed fftw-3.2.1 gsl-1.11 openmotif-2.3.1 and
openmpi-1.2.8
Now, I think everything went fine with the installation (I didn't spot
any terrible warning or errors) but since I'm new to unix commands I'm
Gunnar Widtfeldt wrote:
HI.
I have compiled and installed gromacs 4.0.5 on a mac running 10.5. I
have also installed fftw-3.2.1 gsl-1.11 openmotif-2.3.1 and openmpi-1.2.8
Now, I think everything went fine with the installation (I didn't spot
any terrible warning or errors) but since I'm new
I couldn't find the shell configuration file so I created a file
called .tschrc in my home folder with the line "source /usr/local/
gromacs/bin/GMXRC
That didn't do it. Again I am new to unix commands.
On Jul 13, 2009, at 10:24 PM, Justin A. Lemkul wrote:
Gunnar Widtfeldt wrote:
HI.
I h
Gunnar Widtfeldt wrote:
I couldn't find the shell configuration file so I created a file called
.tschrc in my home folder with the line "source
/usr/local/gromacs/bin/GMXRC
That didn't do it. Again I am new to unix commands.
Try typing it on the command line or open a new terminal.
Maybe th
Gunnar Widtfeldt wrote:
I couldn't find the shell configuration file so I created a file called
.tschrc in my home folder with the line "source
/usr/local/gromacs/bin/GMXRC
Right, because you need to add it - the location of Gromacs is not a standard
location. If you're on a Mac running 1
Thanks,
It works, I had to create the .bash_profile with the line "source /usr/
local/gromacs/bin/GMXRC
On Jul 13, 2009, at 10:47 PM, Justin A. Lemkul wrote:
Gunnar Widtfeldt wrote:
I couldn't find the shell configuration file so I created a file
called .tschrc in my home folder with the
Hi all
I need some monomers get bonds among them, but each one does not have
neither C nor N ends.
Is there any suggestions?
Thank you
--
Jarol E Molina, I.Q., M.S.
Estudiante Doctorado en Ingeniería - Sistemas Energéticos
Universidad Nacional de Colombia - Sede Medellín
jemol...@
Jarol E. Molina wrote:
Hi all
I need some monomers get bonds among them, but each one does not have
neither C nor N ends.
Is there any suggestions?
Assuming that you are trying to create some sort of monomer, read about .rtp
files in the manual, and create the building blocks using the
Justin A. Lemkul wrote:
Jarol E. Molina wrote:
Hi all
I need some monomers get bonds among them, but each one does not have
neither C nor N ends.
Is there any suggestions?
Assuming that you are trying to create some sort of monomer, read about
Edit: *polymer* - Gromacs can handle p
Jarol E. Molina wrote:
Dear Justin
Yes, I Built the .rtp but I can't get the bond between two monomers, I
built the files .tdb and I did not get it.
Then you need to define special terminal units. Perhaps this will be of some
help:
http://lists.gromacs.org/pipermail/gmx-users/2009-Marc
Hi Justin,
I was experiencing the problem before someone suggested using editconf so
I do not think the problem is being caused by editconf. But anyway here
is my editconf command. Let me know if you a source of error in this
command line.
editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
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Hi
I have a question about do_dssp program.is it posible to define the amount
of residus (the percentage) which have specific secondry structure, apart
from the graphic file? if yes what is the the command?
Thanks
--
Tehran University of Medical Sciences
www.tums.ac.ir
--
This message has bee
Hi all gmx-users
I am trying to constraintes some special bonds in em.mdp file for energy
minimization.
But I dont know how can I do it.
Please help me.
Thank you
Mohamad
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http://lists.gromacs.org
Mohammad Ghahramanpour wrote:
Hi all gmx-users
I am trying to constraintes some special bonds in em.mdp file for energy
minimization.
But I dont know how can I do it.
You will need to read about constraints and restraints in chapters 4 and
5 of the GROMACS manual.
Mark
___
Hi hazizian,
That information is stored in the file you get with the option -sc. To
get percentages you have to use awk or something along thos lines.
Cheers,
Tsjerk
On Tue, Jul 14, 2009 at 5:47 AM, hazizian wrote:
>
> Hi
> I have a question about do_dssp program.is it posible to define the amo
I am carrying out energy minimization of the protein peptide complex. But even
after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide
far away from the binding site. This did not happen with ATP-protein complex.
Even in Drug-enzyme tutorial, similar .mdp file is given fo
nikhil damle wrote:
I am carrying out energy minimization of the protein peptide complex.
But even after using nstcomm=1 and/or pbc=xyz, my energy minimized
structure has peptide far away from the binding site. This did not
happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar
I am turning pbc =xyz as written in earlier correspondence. But in spite of
this when i run g_rms after simulation, my initial structure itself shows ~1.5
nm rmsd. So is it a problem at g_rms stage or it is the problem related to PBC
and really the peptide is flying off ??
Regards,
Nikhil
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