Hello again,
That depends on the peptide. There is no general answer. I am starting with
a linear conformations, but that's because I'm working with intrinsically
disordered proteins. That's as far as I can go regarding telling you about
what I'm doing. I'm not at liberty to discuss these things,
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.arch...@gma
Thanks Joao Henriques for helping me with the steps.
On Nov 4, 2013 3:18 PM, "João Henriques"
wrote:
> Hello Archana,
>
> I'm also toying with a TFE-water system, therefore I am also a newbie. This
> is what I am doing, I hope it helps:
>
> 1) Since I'm using G54A7 I created a TFE.itp using GROMO
Erratum:
Where I wrote "I ended up going with the former" it should be "I ended up
going with the latter".
/J
On Mon, Nov 4, 2013 at 10:47 AM, João Henriques <
joao.henriques.32...@gmail.com> wrote:
> Hello Archana,
>
> I'm also toying with a TFE-water system, therefore I am also a newbie.
> T
Hello Archana,
I'm also toying with a TFE-water system, therefore I am also a newbie. This
is what I am doing, I hope it helps:
1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I
don't use PRODGR, see why in DOI: 10.1021/ci100335w).
2) Do the math and check how many molecules
On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote:
Dear Justin,
I have not constructed the system but I have downloaded it from ATB
website. To maintain the number of TFE and water molecules(1:1 v/v) in the
system (I don't want to add extra water molecules) I tried many options in
genbox but
Dear Justin,
I have not constructed the system but I have downloaded it from ATB
website. To maintain the number of TFE and water molecules(1:1 v/v) in the
system (I don't want to add extra water molecules) I tried many options in
genbox but still it adds 678 water molecules. Can you provide me so
On 10/23/13 7:20 AM, Archana Sonawani-Jagtap wrote:
Hi all,
I have never performed TFE-water simulation therfore I want to know after
inserting the peptide in the pre-equilibrated TFE-water mixture, do we need
to adjust the number of TFE or water molecules ?
That depends on how you construc
On 7/17/13 6:26 AM, Archana Sonawani-Jagtap wrote:
Hi Justin,
Thanks...it was really helpful. I saw the
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
Now I don't know how to calculate the number of cosolvents (in my case
TFE for TFE-water in 1:1 vol). Is there any formula
Hi Justin,
Thanks...it was really helpful. I saw the
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents site.
Now I don't know how to calculate the number of cosolvents (in my case
TFE for TFE-water in 1:1 vol). Is there any formula to carry out this
calculation. I can follow other menti
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 previous searches, I got to know that tfe.itp is present in
gmx.ff folder. Can I use this itp file by including it in my top file
generated during pdb2gmx.
Sinc
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