Alright, I understand now.
Many thanks for this!
Antoine
Le 29/08/2012 18:57, Mark Abraham a écrit :
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote:
Many thanks for your quick response, Mark.
So epsilon_r is actually different from the actual relative
permittivity (which would be like 80
Hi all,
Can any one suggest me how to build elastic network model
in gromacs.
Thanks,
Mohan
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Hi Deb,
I recently installed dssp for Gromacs 4.5.4 on RHEL4
You have to just copy the dsspcmbi downloaded from linux distribution to
/usr/local/bin (No need to set an environment variable DSSP if dspcmbi is
in /usr/loca/bin as it is the default path for gromacs)
Rename the dsspcmbi to dssp
Hi Mohan,
Elastic network modeling consists of building a Hessian matrix based
on the distances. That matrix is then diagonalized and the modes are
further investigated. You could write a script to generate a .top file
with a [ bonds ] section, capturing the elastic bonds, and then use
Gromacs to
Hi,
Thanks for a quick reply. In these models we use a distance
cut-off method. Around a particular atom we take a cut-off distance
and connect to all those atoms which fall in the cut-off. I do not
understand, how to connect this atoms with the other atoms falling in
cut-off distance. I have
Hi Mohan,
You need to check chapter 5 of the gromacs manual to understand the
topology format to write. You probably 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
Hi,
I am going through it , i will understand it and try to build
the topology.
Thank you,
Mohan
On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohan,
You need to check chapter 5 of the gromacs manual to understand the
topology format to write. You
On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
Hi,
I am going through it , i will understand it and try to build
the topology.
Fundamentally, harmonic bonds do not serve your purpose, since you need
an interaction that is harmonic in the change in distance, not harmonic
in the
On 30/08/2012 10:17 PM, Mark Abraham wrote:
On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
Hi,
I am going through it , i will understand it and try to build
the topology.
Fundamentally, harmonic bonds do not serve your purpose, since you
need an interaction that is harmonic in
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 mark.abra...@anu.edu.au wrote:
On 30/08/2012 10:17 PM, Mark Abraham wrote:
On 30/08/2012 10:02 PM, mohan maruthi sena
On Thu, Aug 30, 2012 at 1:06 AM, Roland Schulz rol...@utk.edu wrote:
Hi,
the OpenMM code is still under review. You can download it using
I guess you meant OpenMP. As far as I know, the OpenMM build has not
been tested much.
git fetch https://gerrit.gromacs.org/gromacs
Dear all
I am repeating this mail as it could not get uploaded on site. Please
suggest me that whether I can insert 15 residue sequence in an
existing pdb file and can I get the minimized altered coordinates from
here. If not then please suggest an external software or server where
I can model
Hello users,
I'm experiencing trouble using genbox for creating a box of tripeptides in
MARTINI CG polarizable water. I feel like any of the options below should do
the trick, but all give (different) problems.
Generating the randomly place tripeptide box works fine, nothing unusual about
Hi Pim,
I know the problem and also think the problem lies within genbox, but I
haven't been able to trace it. A workaround is to solvate with a small box
containing a single water moleule.
Cheers,
Tsjerk
On Aug 30, 2012 6:12 PM, Pim Frederix pim.frede...@strath.ac.uk wrote:
Hello users,
I'm
Hi Shahid,
You should try homology modeling software, like Modeller.
Cheers,
Tsjerk
On Aug 30, 2012 7:41 AM, shahid nayeem msnay...@gmail.com wrote:
Dear all
Please suggest me a tool with which I can generate insertion mutants
from a .pdb file. I want to insert new 10-15 aa sequence of AA in
Dear Gromacs Users.
Now we areinterested in GROMACS simulation with PROTEIN + DETERGENT as well as
PROTEIN + BILAYER.
Could you let me know if you have any information about DETERGENT Gromos force
field (especially, we think DDM (n-Dodecyl beta-maltose) is best)?
Thanks in advance.
Sangbae.
I've used Macromolecular Builder for inserting loops in proteins. You'll need
further minimization and dynamics to get a relaxed structure though, but that's
where Gromacs comes in.
Erik
30 aug 2012 kl. 18.07 skrev shahid nayeem:
Dear all
I am repeating this mail as it could not get
Hello Gromacs Users:
I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It is completely possible that I am just not
Dear all I am interested in simulating a model of Glycoproteion. I could'nt
find the define of the residue in any forcefield .rtp file of GMX. I am using
Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for
charmm27/ OPLS/Amber99 in gromacs format please respond. Please
On 8/30/12 9:23 PM, Katrina Lexa wrote:
Hello Gromacs Users:
I apologize for asking a question that has come up several times in the
forum, but I have read the answers to those posts and I am not still
unable to fix the error based on the suggestions in the previous emails.
It
On 8/30/12 9:26 PM, 陈应广 wrote:
Dear all I am interested in simulating a model of Glycoproteion. I could'nt
find the define of the residue in any forcefield .rtp file of GMX. I am using
Gromacs 4.5.5 . If any one can help me in getting forcefield parameters for
charmm27/ OPLS/Amber99 in
If I recall correctly, the residue number printed by pdb2gmx is actually the
residue index (starting from zero), so the problematic residue is MLE, which
does have CB.
-Justin
Hi Justin,
Thank you for the fast response. That makes sense, but the problematic
residue is actually both I
Hi Tsjerk,
I am very thankful to you for providing valuable suggestions.
Thank you very much.
On Tue, Aug 28, 2012 at 9:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Ramesh,
You can calculate them from the box matrix, or you can let editconf do that
by simply converting
Dear gmx users.
I asked question about structure factor but I got no reply. I think
it's too basic question,
Then instead, can any one inform me a good reference paper or book why
structure factor must calculate for all atom and not specific types
like O-O, O-C, like rdf does?
Thank you!!
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