Hi ALL,
Is there any way in GROMACS to join two peptide chains by forming a peptide
bond between the C and N atoms?
Any suggestion is welcome.
Regards,
Anirban
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HI
how to calculate SASA of micelle using g_sas?
i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the
atom numbers of micelle.
if micelle is not compact enough but there are no water molecules inside the
micelle, will g_sas calculate the vacancy part inside the micelle?
Or,
Hi all
I would like to know whether Random Accelerator Molecular Dynamics is
available in Gromacs as it is available in AMBER.
E R Azhagiya singam
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HI
As David said,
= How to compute protein-protein interface area?
If you have protein A and B in complex you do three g_sas:
AB AB
A A
B B
the interface is now A + B - AB
I want to calculate protein and ligand aggregate (small micelle of ligand)
interface area.
Is it the same step as
Hi ALL,
Is there any way in GROMACS to join two peptide chains by forming a peptide
bond between the C and N atoms?
Any suggestion is welcome.
Regards,
Anirban
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Hey Lin,
Is it the same step as calculation of protein A and B interface, which David
mentioned above?
But replacing protein B to Ligand aggregate (small micelle of ligand) ?
g_sas -n ligand-micelle-index.ndx ?
Of course.
Is my idea correct?
Is it necessary to always question
Hi Anirban,
If you have the two chains in one file, with identical chain
identifiers and no TER statement in case it's a PDB file, then running
pdb2gmx will actually create the bond between them (no matter how far
away the termini are).
Cheers,
Tsjerk
On Fri, Apr 9, 2010 at 9:37 AM, Anirban
Hi Guillem,
Many thanks for your clarification. I was lazy to find out and remember why
psc0 was not ported to GMX by ffAmber previously and it was exactly because
what you've said.
And because I was not confident enough, I didn't implement that for acpypi,
which I believe does better than
Hi Alan,
I have no experience with acpypi, so I can't tell which one does better,
or why... rdparm not being needed, that would be a strong point.
Unfortunately, I'm running a bit short of time at the moment, so I can't
really spend a lot of time looking into unknown codes, hope you
Hi Guillem!
Thanks! and sorry, you don't need to look the code, just use it when trying
amb2gmx and case you noticed something suspect I would be glad to be
informed. So no need to waste your time other than when *really* needing to
use amb2gmx.
Your solution is what I have in mind and what I am
Hello everybody,
I am going to simulate an enzyme complex taking a
ligand at active site and another ligand at allosteric site. When I ran md
simulation taking ligand at active site only then it was ok. But when I am
running the simulation taking both the ligand it is
abhijit kayal wrote:
Hello everybody,
I am going to simulate an enzyme complex taking
a ligand at active site and another ligand at allosteric site. When I
ran md simulation taking ligand at active site only then it was ok. But
when I am running the simulation
Hi
Thank you for your quick reply. As you mentioned I went through the
mailing list search. And I am thinking my error occured at the system
preparation with taking the two ligands. Earlier I ran md simulation taking
the ligand individually and it was showing no error. So the topolgy I got
abhijit kayal wrote:
Hi
Thank you for your quick reply. As you mentioned I went through
the mailing list search. And I am thinking my error occured at the
system preparation with taking the two ligands. Earlier I ran md
simulation taking the ligand individually and it was showing no
Hi Justin,
No my ligand is different. And my topolgy look like this
#include ffG43a1.itp
#include rrg.itp
#include drg.itp
and at the end it is like this
abhijit kayal wrote:
Hi Justin,
No my ligand is different. And my topolgy look like this
#include ffG43a1.itp
#include rrg.itp
#include drg.itp
and at the end it is like
Dear Mark and Justin,
Thanks for your help, as a beginner to GROMACS i think i have to spend even
more time with each option and make sure i know what i am doing. I will
spend some time by using different electrostatic options with out pbc and
let you know what happens to the simulations.
Thanks
xi zhao wrote:
I would like to run a simulation of a pentamers in a POPC membrane, and
using new inflategro with doughnut mode, but I have met similar result
as the links
http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also
Dear all:
Reading about the gromacs4 manual, I couldn't figure out a way to
apply two sets of pulling simultaneously in gromacs?
I know you can specify a second group using pull_group2, but it has to
use the same reference group in pull_group0, correct? Then I don't
understand how one can
Hi,
Can anybody direct me to where I can find the most recent and updated
version of Mark Abraham's perl scripts for converting CHARMM
parameters to GROMACS?
Many Thanks,
Peter
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Dear Bin:
What you request is not currently possible with any distribution up to
gmx-4.0.7 (I don't know if it is in the cvs). I have a modified
version of gromacs-4.0.5 that will do this, but we are not
distributing it yet. We may upload it in the future for incorporation
into the main
Dear Chris:
Thanks very much for the info.
I will take a look at the source code and see how far I can go.;-)
Bin
On Apr 9, 2010, at 11:38 AM, chris.ne...@utoronto.ca wrote:
Dear Bin:
What you request is not currently possible with any distribution up
to gmx-4.0.7 (I don't know if it is
Hi All,
I send you an email that now I want to remove/delete that but I do't now.my
question is how can I remove my email?
Thank you
_
Hotmail: Trusted email with powerful SPAM protection.
Per the footer of the email:
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
-Justin
you zou wrote:
Hi All,
I send you an email that now I want to remove/delete that but I do't now.
my question is how can I remove my
Dear Users.
Maybe this question is easy for all, but i have problems, patience please.
I do not have experience with metals, now I have a protein (crystal) with
Fe+2, which is coordinating with three HISTIDINES, one D and two molecules
of water, when I try to run pdb2gmx the program tells me
nbsp;nbsp;nbsp;nbsp; nbsp;Hello, I want to construct the oil/water
interface, like this:nbsp;X andnbsp;Y axises of the box are 5 nm, Z axis is
10 nm. 0-5 nm ofnbsp;Z axis in the nbsp;box is water, and 5-10 nm ofnbsp;Z
axis in the box is oil (for example :dodecane), how can I achieve the aim?
Hi
g_sas
By default, periodic boundary conditions are taken into account.
How does g_sas deal with periodic boundary conditions effects? ? ?
Take trjconv an example, I have tried trjconv -pbc ( nojump , whole, atom...
)
or, trjconv -center . I could not get what i wanted.
Thank you
Lin
--
Hi,
are you aware of the Pär's CHARMM version in the GIT version? Unless you
want to do something very special - you probably want to use that over
Mark's version.
Roland
On Fri, Apr 9, 2010 at 2:27 PM, Peter Huwe pjh...@gmail.com wrote:
Hi,
Can anybody direct me to where I can find the
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