http://dx.doi.org/10.1021/ct8000365
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a
On 8/29/18 2:34 PM, Nick Johans wrote:
Thank you dear justin. I'll read the paper. But practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
removed from insulin
Thank you dear justin. I'll read the paper. But practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
removed from insulin 43 residues. The C-terminal carboxyl groups
On 8/29/18 2:13 PM, Nick Johans wrote:
Thank you so much Iris.
want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4
Thank you so much Iris.
want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4 chain?
On Wed, 29 Aug 2018, 22:00 Smith, Iris,
Hi,
You can use multiple types of GPUs in a single run, but it won't be ideal.
Also, with Volta GPUs you'll probably be better off also offloading PME
which won't scale to more than 2-3 GPUs, so probably you'll not want to use
more than 2 GPUs in run with Volta.
--
Szilárd
On Tue, Aug 28, 2018
Hi Nick,
I think the big question is what are you trying to simulate – what is your
goal? It is critical that you now your protein (e.g. how was it crystalized,
any missing atoms, missing residues, hetero atoms, ligands). I think prior to
building your system you should first understand your
Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i
Hi,
I'm a beginner in GROMACS and MD. I used pdb2gmx for having topology file
of PDB ID: 3e7y (lnsuline). It has 4 chains A,B,C,D after pdb2gmx. When you
google it, it is mentioned that insuline has 2 chains named A,B. So why
it's pdb code has 4 chains? Are they couple of each other? If yes and i
Tks for your reply. But this restrain -fc 1000 1000 1000 i ready know it is
using for nvt npt . But for md run. They don't use that restrain. Because i am
going to calculate free energy. Dental G restrain on .
Tin nhắn gốc Từ: Bratin Kumar Das
<177cy500.bra...@nitk.edu.in>
All right. Thanks for reply.
At2018-08-29 20:04:49,Paul bauerwrote:
> Hello,
>
> we have not yet full support for gcc-8, but this is being worked on. You
> can disregard those warnings safely for now.
>
> /Paul
>
> On 29/08/2018 14:01, Du, Yu wrote:
> > Dear gmx-users,
> >
> >
> >
> >
> > I
Hi ,
Gromacs has genrestr programme...In protein-ligand complex tutorial
it is mentioned(how to restrain ligand)
The command is
gmx genrestr -f ligand.gro -o ligand_posre.itp -fc 1000 1000 1000
After that you need to include in the main topology
On Wed 29 Aug, 2018, 12:37 PM Tùng Hoàng,
Hello,
we have not yet full support for gcc-8, but this is being worked on. You
can disregard those warnings safely for now.
/Paul
On 29/08/2018 14:01, Du, Yu wrote:
Dear gmx-users,
I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following
warning:
`make check`
Dear gmx-users,
I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following
warning:
`make check` with regression test set 100% passed. Hope next version will fix
these warnings.
##Warnings##
I think that may indicate that their is something wrong with your input
files, possibly the configuration.
Did you check if the configuration has any bad contacts?
On Wed, Aug 29, 2018 at 7:15 AM sagar bathla wrote:
> hi Dan,
>
> I got the warnings at the start of the mdrun.
>
> Regards
>
Hello all,
I was looking into performing some MD simulations of a DNA molecule - as a
control to simulations of the same DNA molecule along with its binding protein.
However I’m getting a bit confused about how to use temperature coupling
groups. I am torn between simply using one group
What Gibbs energy are you trying to calculate for the system? Of what
process or transformation?
On Wed, 29 Aug. 2018, 3:56 pm abhisek Mondal,
wrote:
> Hi,
> I'm just trying to calculate free energy of a complex system using
> following method:
>
>
hi Dan,
I got the warnings at the start of the mdrun.
Regards
Sagar
On Wed, Aug 29, 2018 at 3:30 PM <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or
Hi Sagar,
At which time step do you get LINCS warnings?
Also, please see:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
Dan
On Tue, Aug 28, 2018 at 3:19 AM sagar bathla wrote:
> Dear all,
>
> My system consists of 2 orthorhombic parallel graphene sheets in a big
Hello everyone,
i am trying to calculate free energy for complex protein-ligand. but in
tutorial it just have methane in water. So i find this
http://www.alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016
but the problem is i don know how to restrain this ligand.
in file complex.top
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