On 6/18/12 5:46 AM, Anik Sen wrote:
Hi This is Anik.
Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The
DNA consisted of a total 10 base pairs. But within the simulation the DNA is
moving inside the solvation box and sometimes it is going outside of the box,
though
On 18/06/2012 7:46 PM, Anik Sen wrote:
Hi This is Anik.
Please choose an email subject more descriptive of your problem. That's
your chance to attract attention!
Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with
water. The DNA consisted of a total 10 base pairs. But withi
Hi This is Anik.
Am using Gromacs 4.5.5 for running dynamics of a DNA surrounded with water. The
DNA consisted of a total 10 base pairs. But within the simulation the DNA is
moving inside the solvation box and sometimes it is going outside of the box,
though due to NVT simulation criteria the p
On 11/01/2012 5:27 PM, Nirmal Prasad wrote:
Dear Mark,
I am facing problem in creating Heme topology...prodrg server is
showing error ,
This is a GROMACS mailing list, so we're generally unable to help with
that. We certainly can't help if you don't tell us details about the error.
can y
Dear Mark,
I am facing problem in creating Heme topology...prodrg server is
showing error , can you please tell how to solve this problem or can
you please provide the heme topology
here are the PDB coordinates for HEME
Dear Mark,
Thank you very much..now its working
nirmal
On Tue, Jan 10, 2012 at 5:31 PM, Mark Abraham wrote:
> On 10/01/2012 10:37 PM, Nirmal Prasad wrote:
>
> I got this message "pdb2gmx: command not found"
>
> but I installed gromacs..how to solve this error
>
>
> You need a functional PATH.
On 10/01/2012 10:37 PM, Nirmal Prasad wrote:
I got this message "pdb2gmx: command not found"
but I installed gromacs..how to solve this error
You need a functional PATH. See
http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation.
Mark
nirm
I got this message "pdb2gmx: command not found"
but I installed gromacs..how to solve this error
nirmal
On Tue, Jan 10, 2012 at 3:48 PM, Mark Abraham wrote:
> On 10/01/2012 9:12 PM, Nirmal Prasad wrote:
>
> Dear Gromacs users...
>
> I am new to gromacs...
>
> I have not understood this
>
> "
>
On 10/01/2012 9:12 PM, Nirmal Prasad wrote:
Dear Gromacs users...
I am new to gromacs...
I have not understood this
"
In your shell configuration file (e.g. .bashrc for bash or
.cshrc/.tcshrc for tcsh) you should use a command analogous to:
source /usr/local/gromacs/bin/GMXRC
near the end
Dear Gromacs users...
I am new to gromacs...
I have not understood this
"
In your shell configuration file (e.g. .bashrc for bash or .cshrc/.tcshrcfor
tcsh) you should use a command analogous to:
source /usr/local/gromacs/bin/GMXRC
near the end of that file.
"
can any one please tell me what
On 9/01/2012 6:54 PM, Nirmal Prasad wrote:
Dear Mark,
Thanks for responding.
I am new to Gromacs.
I am working on Cytochrome P 450 proteins, these proteins contain HEME group.
For MD run should I prepare separate protein and HEME group topologies
and reconstruct protein-HEME complex. Is this
Dear Mark,
Thanks for responding.
I am new to Gromacs.
I am working on Cytochrome P 450 proteins, these proteins contain HEME group.
For MD run should I prepare separate protein and HEME group topologies
and reconstruct protein-HEME complex. Is this procedure is correct or
not.
nirmal
On 1
On 9/01/2012 6:42 PM, Nirmal Prasad wrote:
Hello,
I am working on Heme containing proteins, is it necessary to treat
Heme group as Ligand.
What do you mean by "treating as a ligand"?
Mark
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Pl
Hello,
I am working on Heme containing proteins, is it necessary to treat
Heme group as Ligand.
Best
nirmal
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pawan raghav wrote:
I am attaching the config file which is generated on my system by using
fftw-2.1.5. Please notify me where is the mistake.
For future reference, ZIP archives can be inconvenient for some users (we use
primarily Mac and Linux systems). There is no need to zip up a log f
uld have peptide
displaced ?
Regards,
Nikhil
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Tuesday, 14 July, 2009 12:28:05 PM
Subject: Re: [gmx-users] Hello
nikhil damle wrote:
> I am turning pbc =xyz as written in earlier correspondence.
nikhil damle wrote:
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? You need to compare that with pre-simulation...
So is it a problem at g_rms stage or it is the
problem r
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Tuesday, 14 July, 2009 12:07:24 PM
Subject: Re: [gmx-users] Hello
nikhil damle wrote:
> I am carrying out energy minimization of the protein peptide complex. But
> even after using nstcomm=1
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 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
Hi Nehme,
> Also, in our zinc finger models, the zinc plays a structural role and it is
> not implicated in DNA recognition. Furthermore, I will read your paper and
> the references. I looked in the Literature and from NMR studies/X-ray and MD
> done on zinc fingers containing a zinc ion coordinat
Hi Nehme,
I've did simulations on TRAIL, which also contains a zinc-finger
domain, involving three cysteines and a chloride ion. But it's not so
simple. Luckily the exact parameters seemed not that vital, as the
zinc apparently functions to keep the three subunits together and was
in any case not
Hi,
Have a look at
http://wiki.gromacs.org/index.php/Parameterization
and
http://wiki.gromacs.org/index.php/Exotic_Species
Next to that, also consider that you are talking about a site with -2
formal charge (ZnS4)2-. How likely is that? From QM studies, it seems
much more likely that there are 1
Nehme El Hachem wrote:
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields for
that type of complexes (the zinc ion is coordinated to 4 deprotonated
cysteines)?
The first step is probably to search in the literature for anything similar.
Has anyone attempted such wo
Hello,
I have a DNA-Zinc finger complex. What are the suitable forcefields
for that type of complexes (the zinc ion is coordinated to 4
deprotonated cysteines)?
I need to do some molecular minimization and dynamics including the
nucelic acid sequence.
Looking for some help.
Thank you.
Ne
Hi Anamika,
It would be good to do some background reading on MD. For this issue,
you most likely should read:
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Cheers,
Tsjerk
On Feb 12, 2008 11:14 AM, Anamika Awasthi <[EMAIL PROTECTED]> wrote:
> Dear Gromacs users,
> I am b
Quoting Anamika Awasthi <[EMAIL PROTECTED]>:
> Dear Gromacs users,
> I am beginner in using using GROMACS and MD simulations, Please help
> me in solving my problem.
> I simulate my protein for 5 ns and after simulations RMSD in C-alpha is
> showing a big fluctuation after 3 ns and til
Dear Gromacs users,
I am beginner in using using GROMACS and MD simulations, Please help
me in solving my problem.
I simulate my protein for 5 ns and after simulations RMSD in C-alpha is
showing a big fluctuation after 3 ns and til 3.5 ns to 4.5 ns its fine and
again its showing fluctua
On Tue, 11 Dec 2007 04:54:51 -0800 (PST)
Farzad Molani <[EMAIL PROTECTED]> wrote:
Hi dear
I'm going to compute PMF for two amins by free energy perturbation but
I don't know what do I?
please help me.
check the tutorials ...
thanks in advance.
Hi dear
I'm going to compute PMF for two amins by free energy perturbation but
I don't know what do I?
please help me.
thanks in advance.
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