If you want the lipid connected to the amino acid, i think it would be a good
idea to add a new residue type to aminoacids.rtp which contains both, your
lipid and the amino acid its connected to. You can start from the rtp entry of
the amino acid and add the lipid parameters. After doing that, y
Hi,
"Every charge group must be a subset of an energy group or fully disjoint
from it."
Does it mean that I could not set up the HBD and HBA in the ligand at the
same time, but the HBD in ligand and HBA in lipid bilayer could be
calculate?
or Each atoms in the ligand must belong to the disjointed
I have some questions regarding editconf:
1)If we did'nt mentioned -box parameters,the *default vectors are 0 0
0*, why it is zero and what does it mean?
2)How to determine distance between the solute and the box, is it
appropriate to take it 0.9 nm for
a globular protein of 179 amino acids.
After
Hi Nuno,
I have still problems with the insatllation of the 4.0.7 version.
After unpacking of fftw and gromacs, I did:
In the fftw folder:
./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared
--enable-float
make -j
make install
export CPPFLAGS="-I$HOME/local/fftw3/include"
expor
Hi Thomas, please send the complete config.log. After you try what I
suggest bellow.
I guess the environment variables for compilers and libs are not set
correctly, not your fault, we'll check on the config file.
#make sure your're usnig bash
bash
#export the regular variables
export CPPFLAGS="-
On Thu, 2011-03-17 at 10:44 +0100, Thomas Koller wrote:
> Hi Nuno,
>
> I have still problems with the insatllation of the 4.0.7 version.
>
> After unpacking of fftw and gromacs, I did:
>
> In the fftw folder:
>
> ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-shared
> --enable-f
On 17/03/11, bipin singh wrote:
>
> I have some questions regarding editconf:
>
> 1)If we did'nt mentioned -box parameters,the default vectors are 0 0 0, why
> it is zero and what does it mean?
>
>
It means no box is defined.
>
> 2)How to determine distance between the solute and the b
Hi Thomas,
the error you see indeed suggests that something is messed up with
your compiler. In your case however I think that is due to the CPPFLAGS
and LDFLAGS you set. Those sometimes mess with the configure makros.
Try
export CPPFLAGS=
export LDFLAGS=
export LD_LIBRARY_PATH=
to erase what yo
Now I get this again:
checking for fftw3.h... configure: error: Cannot find the default external FFT
library (fftw3).
Please follow my way:
i) I unpacke fftw and gromacs to two folders.
iii) I go the the fftw folder and make:
- ./configure --prefix=$HOME/local/fftw3 --enable-sse --enable-sh
On 17/03/11, Thomas Koller wrote:
> Now I get this again:
>
> checking for fftw3.h... configure: error: Cannot find the default external
> FFT library (fftw3).
>
>
>
> Please follow my way:
>
> i) I unpacke fftw and gromacs to two folders.
> iii) I go the the fftw folder and make:
>
You got this wrong
export CPPFLAGS="-I/home/local/fftw/include"
export LDFLAGS="-L/home/local/fftw/lib"
replace by this
export CPPFLAGS="-I$HOME/local/fftw/include"
export LDFLAGS="-L$HOME/local/fftw/lib"
On Thu, Mar 17, 2011 at 12:24 PM, Thomas Koller wrote:
> Now I get this again:
>
> checkin
Thomas Koller wrote:
Now I get this again:
checking for fftw3.h... configure: error: Cannot find the default external FFT
library (fftw3).
Please follow my way:
i) I unpacke fftw and gromacs to two folders.
iii) I go the the fftw folder and make:
- ./configure --prefix=$HOME/local/fftw3
On 17/03/11, Diego Enry wrote:
> You got this wrong
> export CPPFLAGS="-I/home/local/fftw/include"
> export LDFLAGS="-L/home/local/fftw/lib"
>
> replace by this
> export CPPFLAGS="-I$HOME/local/fftw/include"
> export LDFLAGS="-L$HOME/local/fftw/lib"
>
This is immaterial if Thomas installed t
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> http://www.gromacs.org/Support/Mailing_Lis
hello
I am using OPLS AA FF and my protein contains a non standard amino acid CSD
for which the topology parameters are not present . Can someone tell how to
include CSD into topology file?
ashu
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ashutosh srivastava wrote:
hello
I am using OPLS AA FF and my protein contains a non standard amino acid
CSD for which the topology parameters are not present . Can someone
tell how to include CSD into topology file?
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Fo
Dear Elisabeth,
I'm going to make some general remarks on what I would consider a
reasonable set of choices for such simulations:
(1) 3x3 nm in the xy plane seems perfectly fine to me if your model systems
is made up of some well-behaved molecular liquid, alkanes for instance.
(2) GROMACS manual
Dear All,
I'm running set of umbrella sampling simulations to get the PMF of a
disaccharide binding to a protein.
I followed the tutorial provided by Justin and changed the values of
necessary parameters according to my system.
The mdp file for umbrella sampling simulations is as follows:
-
Dear all,
thanks a lot for your suggestions that give me the possibility to improve my
calculation.
All the best
Anna
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Please search the archive at
http://www.gromacs.org/Support/Mailing_List
Sai Kumar Ramadugu wrote:
Dear All,
I'm running set of umbrella sampling simulations to get the PMF of a
disaccharide binding to a protein.
I followed the tutorial provided by Justin and changed the values of
necessary parameters according to my system.
The mdp file for umbrella sampling sim
Hi Felix,
Thank you for your help.
Hi Justin,
I did not want to write a long e-mail describing what I did and what did not
work. All I wanted to learn was whether there was some more detailed
information somewhere that I can reach. You do not have to reply to an email
if you feel it is not worth
Emine Deniz Tekin wrote:
Hi Felix,
Thank you for your help.
Hi Justin,
I did not want to write a long e-mail describing what I did and what did
not work. All I wanted to learn was whether there was some more detailed
information somewhere that I can reach. You do not have to reply to an
em
Dear GROMACS user,
Hello. I am new to molecular dynamics simulation, and also to simulation of
interface. Recently I have simulated liquid-vapor interface of heptane in a
slab with NVT ensemble, and liquid-liquid inteface of water-heptane in NPzAT
ensemble. I am using GROMOS force field and SPC/E
Dear GROMACS users and developers,I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy:g_energy -f md1_vis.edr -o md1_vis_1perv.xvgthe output:Statistics over 101 steps [ 0. through 2000. ps ], 1 data setsAll statistics are over 11 pointsEner
Alif M Latif wrote:
Dear GROMACS users and developers,
I'm having trouble getting values for my 1/viscosity calculation which
obtained from g_energy:
g_energy -f md1_vis.edr -o md1_vis_1perv.xvg
the output:
Statistics over 101 steps [ 0. through 2000. ps ], 1 data se
Hi,
I did a simulation of 5ns ... after viewing the trajectory in VMD , some
loop regions seems to be stretched like a straight wire.. But when I made a
movie using trjconv and viewed in pymol.. the structure seems to be fine..
So, shall I continue my analysis assuming the structure to be fine ...
bharat gupta wrote:
Hi,
I did a simulation of 5ns ... after viewing the trajectory in VMD , some
loop regions seems to be stretched like a straight wire.. But when I
made a movie using trjconv and viewed in pymol.. the structure seems to
be fine.. So, shall I continue my analysis assuming t
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