Dear Gromacs friends,
I want to simulate a system containing the biotin.
I get the topology from ATB.
I want to validate these toplogy for my use .
So please could some one told me the way how I can do it ??
I never had any such experience.
Is these is any tutorial regarding to these.
T
Dear users,
I apologise if this is a stupid question, however after a morning of
searching I have not been able to find the answer.
1. I have a sample itp file and it contains a section like this:
[ atomtypes ]
CF CF 6 12.011000.2588 A3.5e-01 2.56134e-01
HF
There is nothing stopping you from replacing the ion in your binding
pocket with the original water and then replacing another water elsewhere
with the ion at the oxygen's coordintes, then running genconf to renumber
the gro file.
On 2012-11-26 06:25:47PM -0800, Yun Shi wrote:
> I did hope the ion
I did hope the ions will move out eventually.
But after my ~70ns of conventional MD (with duplicate MD runs and the
protein as a dimer with identical sequence), they were still there in
the binding site.
So I assume it would be much better to start without any salt ions
beside my ligand.
Could a
On 11/26/12 2:08 PM, Albert wrote:
hello:
I am going to calculate the number of water molecules within 6 A of
residue 114 by following command:
g_select -f md.xtc -s npt3.pdb -os size.xvg -select "resid 114 and rdist
< 0.6"
but it said:
WARNING: masses and atomic (Van der Waals) radii
On 2012-11-26 21:28, Yun Shi wrote:
Hi everyone,
I am doing conventional MD of a protein-ligand system with a mobile
loop as part of the binding site.
Presumably, the positive Arg side chain on the mobile loop will
eventually move towards the negative carboxylic group on my ligand.
But I found
A good start might be:
Phys. Chem. Chem. Phys., 2011, 13, 10437–10448
This paper is about hybrid-models (mixing CG and AA). But they discuss
'boltzmann inversion' and 'force matching', which are both methods to
obtain CG-potentials.
Since they use small molecules it focusses on nonbonded interac
hello:
I am going to calculate the number of water molecules within 6 A of
residue 114 by following command:
g_select -f md.xtc -s npt3.pdb -os size.xvg -select "resid 114 and rdist
< 0.6"
but it said:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on r
You need to name libraries with FFTW3F_LIBRARIES, not the library path.
That explains the dropped dependency and subsequent problems.
Mark
On Mon, Nov 26, 2012 at 4:19 PM, Stefan Jasconek <
stjas...@students.uni-mainz.de> wrote:
> Dear Users,
> I have problems with the installation of GROMACS 4.
the distance distribution should be given by the Boltzmann factor of the
potential energy function between the beads, assigning V(r)=0 for the most
probable distance in your histogram. that's what you get when you take a
molecule in vacuum and for instance you compare the dihedral distribution
with
Dear Justin,
I am very thankful to you for your reply, you are correct, I have plotted
the histo.xvg file in wrong manner. After plotting histograms in correct
manner I have realized that my sampling is very poor as histograms and
there overlapping is restricted to some regions only, no histogram
hello:
I am going to calculate the number of water molecules within 6 A of
residue 114 by following command:
g_select -f md.xtc -s npt3.pdb -os size.xvg -select "resid 114 and rdist
< 0.6"
but it said:
WARNING: masses and atomic (Van der Waals) radii will be determined
based o
Dear Users,
I have problems with the installation of GROMACS 4.5.5 on MacOS 10.7.5.
GCC version 4.2.1
FFTW is: FFTW-3.3.2.
The CMAke command
cmake -DGMX_THREAD_MPI=OFF \
-DFFTW3F_INCLUDE_DIR=$FFTWDIR/include \
-DFFTW3F_LIBRARIES=$FFTWDIR/lib \
-DGMX
Hi dear GROMACS experts
I wanna know if GROMACS uses only Maxwell-Boltzmann distribution
in statistical mechanics, or it also uses Fermi-Dirac and Bose-Einstein
statistics.If it only uses Maxwell-Boltzmann distribution, are the results
reliable and correct? I mean can we use this law, which is b
On 11/26/12 9:43 AM, Venkat Reddy wrote:
Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?
I have no idea. I haven't used PRODRG in a very long time
Thank yo Justin for your help...I have generated the same topology using *ATB.
*Now, I got the masses correctly (as pointed out by you). So, I'm afraid
that is there any bug in PRODRG server?
On Mon, Nov 26, 2012 at 8:09 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:35 AM, Venkat Reddy wrote:
>
On 11/26/12 9:35 AM, Venkat Reddy wrote:
Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?
PRODRG doesn't even do a very good job of being compatible with 43A1, so
Dear Justin,
One more doubt. I am using Gromos 53A6 ff. Can I use Prodrg to generate
topology for my ligand? Because, I guess, prodrg uses Gromos 43A1. Can I
mix 53A6 and 43A1?
On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
Thanks Justin...I will certainly do.
On Mon, Nov 26, 2012 at 7:46 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 9:12 AM, Venkat Reddy wrote:
>
>> Dear Justin,
>> I haven't touched the *Mass column.* I have edited the charges only using
>> "gedit" in linux.
>>
>>
> Regardless, the masses I pointed
On 11/26/12 9:12 AM, Venkat Reddy wrote:
Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.
Regardless, the masses I pointed out are wrong. You should still do the test to
#include the original topology and see if it works, then if it d
Dear Justin,
I haven't touched the *Mass column.* I have edited the charges only using
"gedit" in linux.
On Mon, Nov 26, 2012 at 7:35 PM, Justin Lemkul wrote:
>
>
> On 11/26/12 12:58 AM, Venkat Reddy wrote:
>
>> Dear all,
>> I am simulating a Protein-Drug complex. I am following Justin's tutori
On 11/26/2012 02:36 PM, David van der Spoel wrote:
It's posted on the website.
http://www.gromacs.org/Downloads/User_contributions/Other_software
You want this one:charmm2gromacs-pvm.py
--
thanks a lot for kind reply.
But how to use it? I am trying to run with command:
python charmm2gr
On 11/26/12 1:03 AM, ramesh cheerla wrote:
Dear Gromacs users,
I am calculating PMF for the ion permeation through a tunnel, using
umbrella sampling. In my system I have some binding sites with ions, I have
removed some ions from binding sites before pulling and In pulling
simulations
On 11/26/12 6:01 AM, SANTU BISWAS wrote:
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS wrote:
dear users,
When performing a energy minimization of a
polypeptide(formed by lysine-5-residues) in vacuum box by using
Steepest Descent and also Conjugate Gradient methods in gromacs
On 11/26/12 12:58 AM, Venkat Reddy wrote:
Dear all,
I am simulating a Protein-Drug complex. I am following Justin's tutorial. I
have used *PRODRG *for generating topology. *Gaussian *has given me the ESP
charges. I have edited the charges in the itp file using the *Gaussian*'s
ESP charges*. *Th
Or run any binary with the -version option e.g:
$ mdrun -version
--
Szilárd
On Sun, Nov 25, 2012 at 10:30 AM, Mark Abraham wrote:
> Look at the top of the output of any GROMACS program.
>
> Mark
>
> On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett
> wrote:
>
> > Dear All,
> >
> > Is any gromacs c
On Sun, Nov 25, 2012 at 8:47 PM, Thomas Evangelidis wrote:
> Hi Szilárd,
>
> I was able to run code compiled with icc 13 on Fedora 17, but as I don't
> > have Intel Compiler v13 on this machine I can't check it now.
> >
> > Please check if it works for you with gcc 4.7.2 (which is the default)
> a
This should be in the pullf.xvg (time and then the forces).
Am 24.11.2012 19:55, schrieb gmx-users-requ...@gromacs.org:
Hi to all gromacs users,
I am trying to run an umbrella sampling and i am getting the initial
conformations by pulling simulations but i want to check the simulation throug
On 2012-11-26 12:00, Albert wrote:
Hello:
I found that someone mentioned that there is a script from Mark which
could be used to convert CGenff format into Gromacs .itp file. I
searched the mailist and didn't find it.
I am just wondering where can I obtain this script?
thank you very much
On Sun, Nov 25, 2012 at 9:08 PM, SANTU BISWAS wrote:
> dear users,
>
>When performing a energy minimization of a
> polypeptide(formed by lysine-5-residues) in vacuum box by using
> Steepest Descent and also Conjugate Gradient methods in gromacs double
> precision,i noted that GROMA
Hello:
I found that someone mentioned that there is a script from Mark which
could be used to convert CGenff format into Gromacs .itp file. I
searched the mailist and didn't find it.
I am just wondering where can I obtain this script?
thank you very much
best
Albert
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