Hello everyone,
I am getting the following error when i execute
grompp command ,can anyone please explain me why this error arises,
*NOTE 2 [file ile.top, line 2986]:
The bond in molecule-type Protein_chain_I between atoms 22 N and 23 HN
has an estimated oscillationa
Hi all,
I try to build go model(which uses only c-alpha atoms), my pdb
contains only c-alpha atoms extracted from the original pdb file ,when i
use pdb2gmx command on c-alpha containing pdb file it gives the following
error.
Atom N is used in an interaction of type atom in th
Hi all,
I want to define a potential form and give it as input for which
i have seen manual ,thought gromacs table option is fine, i have an example
of generating 9-6 potential form , My question is how to generate
table.xvg, what is the command to generate table.xvg from code table.c.
Hi all,
I use a user defined potential to describe non-bonded
interactions, as this excludes i, i+2,i+3. If i want to describe a user
defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give
that in mdp file.
T
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Hi all,
I use a user defined potential to describe non-bonded
interactions, as this excludes i, i+2,i+3. If i want to describe a user
defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give
that in mdp file.
Thanks for a reply in advance
Hi all,
I have learned from manual that non bonded interactions can be
given as user defined potential by using tables. If i want to give dihedral
term as user defined potential keeping rest of the bonded parameters in
their usual form, how can i do that.
Please suggest me a way,
Tha
Hi all,
I am using a user defined potential to describe non-bonded
interactions, which describes attractive potential for residues separated
by four or more bonds . Now I want to describe a user defined
potential(repulsive) for atoms falling with in three residues and which are
not determ
Hi all,
I have used a user define potential to describe attractive
potential beyond i and i+3 atoms(similar to lLJ). If i want to describe
repulsive interactions with in i and i+3 , how can i do it in gromacs? can
anyone suggest me a way,
Thanks and Regards,
Mohan
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Hi all,
My pdb file contains only c-alpha atoms , i have named alternate
CA atoms(res) as CB(1res CA,2res CB,3res CA...) , I have given my residue
name as ALB, accordingly i have changed .rtp ,atomtype
files,residuetype.dat. i want to use force field(charmm27.ff) present in
current direc
Hi all,
I am using tabulated potential option for non bonded
interactions. The system that i am using contains on CA(alpha) CB(beta)
,atoms connected, If i use option
energygrps = CA CB
energytable = CA CA CB CB it caluclates potential
between
Hi all,
I have system consisting of a peptide(alpha-helix), I want the
peptide to be surrounded by magnesium ions(instead of water). How can i do
this gromacs? How can I find the concentration of magnesium ions. just like
in solution we have 0.5 Molar Mg+2 solution, My question how can
Hi ,
Thanks for a quick reply. Sorry for not being clear, I want to
surround the peptide with just ions(sodium). How can I do this?
Thanks,
Mohan
On Thu, May 2, 2013 at 4:58 PM, Justin Lemkul wrote:
>
>
> On 5/2/13 12:38 AM, Mohan maruthi sena wrote:
>
>> Hi all
Hi all,
I want to perform brownian dynamics simulations using gromacs
4.5.5 for a system containing protein in water. What is the basis to
select the bd_fric value for this system. I came to know through previous
posts that a value of 3000 would be fine for a time step less than 4fs. M
rt with? See manual for details
> of how this trick works.
>
> Dr. Vitaly Chaban
>
>
>
>
>
> On Wed, May 29, 2013 at 11:48 AM, Mohan maruthi sena <
> maruthi.s...@gmail.com
> > wrote:
>
> > Hi all,
> > I want to perform brownian dynamics simu
Hi all,
I want to create an elastic network model for a protein,
in which i have selected only c-alpha atoms(removed rest of the
atoms). To attach a spring between alpha atoms with some
force(spring) constant k , How can i mention this in topology file ?
Thanks,
Mohan
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gmx-u
Hi all,
I want to prepare a basic elastic network model (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein
and considered only streching potential(k.(b-b0)^2)) and removed
rest of angle,dihedral,non bonded interactions. I have mentioned a
bond betw
Hi all,
I want build a toplogy for a protein , for which , each and
every atom has to make bonds with other atoms with in certain
specified cut-off distance. How can i do this ?
Please suggest me a way,
Thanks in advance,
Mohan
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htt
doable. Note that this
> will NOT emulate angles or dihedrals, just the stretching term. I can't
> understand why you would want bonds between all atoms within a certain
> distance, however, and I hope you know what you're doing.
>
> Erik
>
> 25 aug 2012 kl. 06.54 skrev
Hi all ,
Can any one suggest me how to build elastic network model
in gromacs ( any literature,tutorial kind).
Thanks in advance,
K.Mohan
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Hi all,
I want to build elastic network model for a protein. To
build an Elastic network model , I consider only C-alpha atoms of the
protein. I want to make c-alpha atoms connect(make bond) with all the
other c-alpha atoms , if it falls within certain cut-off distance.
How can i do t
he ones
> that are within a cut-off distance of your choice and then write a list of
> bonds that you could add to a gromacs topology file ...
>
>
> On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote:
>
>> Hi all,
>>I want to build elastic network model for
Hi all,
Can any one suggest me how to build elastic network model
in gromacs.
Thanks,
Mohan
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http://www.gromacs.org/Support/Mailing_Lists/Search be
egrator, be warned that
> these models are very incomplete and are intended to only capture the
> tangents around the starting structure.
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Aug 30, 2012 at 9:22 AM, mohan maruthi sena
> wrote:
>> Hi all,
>>
robably need only to define one atom
> type and the C6/C12 parameters could probably even be set to zero. You
> need to write an [ atoms ] section, and a [ bonds ] section, according
> to the specifications in the manual.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Aug 30, 2012
Hi ,
Thank you very much .I will take all these factors in to
account while building the model.
Thank you,
Mohan.
On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham wrote:
> On 30/08/2012 10:17 PM, Mark Abraham wrote:
>>
>> On 30/08/2012 10:02 PM, mohan maruthi sena wr
) with respect to elastic network model.
Thank you,
Mohan
On Thu, Aug 30, 2012 at 5:58 PM, mohan maruthi sena
wrote:
> Hi ,
> Thank you very much .I will take all these factors in to
> account while building the model.
>
> Thank you,
> Mohan.
>
> On T
Hi all,
I am trying to build an elastic network model using only
C-alpha atoms . Potential energy function contains only bond
stretching energy term rest like angle,dihedral and non bonded are not
included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond
potential . The probl
Hi all,
I want to build elastic network model using gromacs. I consider
only c-alpha atoms and only bond stretching term contributes to towards
potential energy. Bonds are connected between atoms present with in
certain cut-off distance(modified topology accordingly). When I run md t
Hi Neumann,
You can use tabulated potential option in
gromacs. Please check the site given below:
http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
Thanks,
Mohan
On Fri, Jun 7, 2013 at 3:38 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I want to
Dear gmx users,
I would like to calculate persistence length of
DNA using gromacs command g_polystat . The out put file of persists.xvg
contains persistence length in number of bonds and it shows that the
average persistence length = 4.3 bonds. How can we convert no of b
putational
> Biophysics<http://www.mpibpc.mpg.de/home/grubmueller/index.html>,
> |
> | Am Fassberg 11, 37077 Goettingen, Germany |
> | Tel.: +49 551 201 2304|
> |====|
>
>
> On Su
Hi all,
I want to calculate the persistence length of whole DNA
molecule. I know that we can calculate it by using option g_polystat -f
.trr -p p.xvg , but I am not able to figure out what set of of atoms I have
to select while making the index, so that I could get persistence length o
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