Should I start with helical peptides and see if it maintains the helicity
or I can start with random coil?
Do random coil peptides take long simulation time to form helical peptides?
any help on this will be appreciated.
On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap <
ask.a
Lund University
> Lund, Sweden
> ----
> joao.henriq...@teokem.lu.se
> http://www.teokem.lu.se/~joaoh/
>
>
> On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul wrote:
>
> >
> >
> > On 10/24/13 1:13 PM, Archana Sona
de me some hint?
Is their need to remove periodicity of this pre-equilibrated system as in
case of lipids?
Regards,
Archana
On Wed, Oct 23, 2013 at 5:26 PM, Justin Lemkul wrote:
>
>
> On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
>
>> Hi all,
>>
>> I have n
is welcome.
Thank you.
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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thank you so much. It was such a stupid error from my side.
On Fri, Oct 18, 2013 at 5:08 PM, Justin Lemkul wrote:
>
>
> On 10/18/13 2:54 AM, Archana Sonawani-Jagtap wrote:
>
>> Hi,
>> This is my input file for calculating bilayer thickness in absence of
>> pep
without peptide)
When running in Gnuplot I get following error:
splot 'output.frame1.20x20.average_thickness.dat' matrix using (1+$1):(1+$2):3
Warning: empty x range [1:1], adjusting to [0.99:1.01]
Please help me.
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informat
l be printed to
output.frame1.200x198.bottom_a reas.dat
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
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same manner
as Justin's KALP tutorial skipping the peptide insertion part?
Please help me...
thanks in advance
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
--
gmx-users mailing listgmx-users@gromac
the lateral
area of system and APL.(keeping thickness as no)
which lateral area has to be considered as the thickness of the bilayer in
terms of nm? both have different values. I am confused.
which values should be reported for thickness and APL?
Please help me.
--
Archana Sonawani-Jagtap
Thank you.
On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul wrote:
>
>
> On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
>
>> I have simulations for different peptides in POPC bilayer.
>>
>> I want to calculate pair distribution function (pdf) between negativel
calculate the center of mass for a bilayer?
Any help is highly appreciated.
--
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx
other mentioned steps.
Thanks in advance.
On Wed, Jul 17, 2013 at 2:41 PM, Justin Lemkul wrote:
>
>
> On 7/17/13 1:03 AM, Archana Sonawani-Jagtap wrote:
>>
>> HI,
>>
>> I want to simulate helical peptide in TFE-water (1:1 vol) solvent.
>>
>> 1. From previo
-equilibrated system
from ATB site. I dont know if I can use either this pdb or gro file
during genbox step for -cs flag
Can anyone help me out in this regard.
Thanks in advance.
Regards,
Archana Sonawani-Jagtap
Senior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India
perform (de)coupling
of the ligand in complex with the receptor and in bulk solution. I don't
know exactly how to start with this process.
Do I need only the protein-ligand complex simulated for 5ns to start with?
Thanks in advance.
--
Archana Sonawani-Jagtap
Junior Research Fellow,
Biome
t;
> I also asked the similar question. Alex replied :" I would start
> several (5-10?) runs with different (random) starting impulse to get
> more reliable data."
>
> Best
>
> Shiyong
>
>
> On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani
> wrote:
>
around 6.3 nm2 throughout the simulation which is very high.
This is very contradicting result. Is something wrong in the simulation?
Thanks in advance.
--
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
--
gmx-users
at 8:00 PM, Justin Lemkul wrote:
>
>
> On 9/28/12 9:27 AM, Archana Sonawani wrote:
>
>> Hi,
>>
>> I have performed simulations for 3 different ligands complexed with the
>> same protein. I want to compare the binding energies of these different
>> three c
uu.se
> http://www2.icm.uu.se/molbio/elflab/index.html
>
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Hi,
Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.
On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD <
luis.pinedadecas...@lnu.se> wrote:
> On 09/25/2012 10:08 AM, naga sundar wrote:
>
>> Dear Felipe
>>
>> Thanks for
. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
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>
--
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339
--
gmx-users mail
Dear Sir/madam,
I have a ligand molecule for which I generated the topology file using
Prodrg software. As the charges and groupings provided by Prodrg are not
much reliable. I need to assign correct charges and groupings for my
ligand. I had referred the article "Practical considerations for buil
Dear Sir/Madam,
For orienting the protein and membrane, I have used the .mdp and following
topology file:
;
; File 'topol_popc.top' was generated
; By user: jalemkul (502)
; On host: bevany.biochem.vt.edu
; At date: Fri Oct 20 13:26:53 2006
;
; This is your topology
Hello,
I have run 10 ns simulation for ligand-receptor complex. For analysis, I
checked RMSD, Radius of gyration, Hydrogen bonds and distance using g_dist.
In the RMSD plot, the whole simulation shows RMSD between 0 - 0.5nm , but
after 5ns I get long vertical lines upto 2.5 nm. I dont know whats
Hi,
I am performing MD simulations for peptide(ligand)-receptor complex. I
dont know how to calculate the binding energy for the complex and individual
structures using gromacs version 4.
Can anyone please help me out.
Regards,
Archana.
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