On Mon, 26 Nov 2018, 21:28 Justin Lemkul
>
> On 11/26/18 10:51 AM, Nick Johans wrote:
> > On Mon, 26 Nov 2018, 18:22 Justin Lemkul >
> >>
> >> On 11/22/18 11:41 AM, Nick Johans wrote:
> >>> Hi
> >>>
> >>> I am beginner in
On Mon, 26 Nov 2018, 18:22 Justin Lemkul
>
> On 11/22/18 11:41 AM, Nick Johans wrote:
> > Hi
> >
> > I am beginner in MD. Maybe it is not a wise question but i want to
> > calculate the interaction energy between protein and ligand and also PMF
> in
> > dif
Hi
I am beginner in MD. Maybe it is not a wise question but i want to
calculate the interaction energy between protein and ligand and also PMF in
different distances. But i don't know what is the didference between PMF, i
mean free energy in particular(by umbrella sampling) and the interaction
ene
Thank you dear justin, finally you answer me;)
On Thu, 13 Sep 2018, 16:59 Justin Lemkul, wrote:
>
>
> On 9/13/18 7:55 AM, rose rahmani wrote:
> > Hi,
> >
> > I recieved an email from GROMACS, says the message is too big(because of
> > many replies). So what should i do to continue my discussion?
Sorry i'm nick's friend and i couldn't access to my email so i had to send
it by his account.
Rose
On Wed, 12 Sep 2018, 20:16 Nick Johans, wrote:
> Thank you so much Joao for detailed answer. You are right, i think i
> should write my own code. But since i don'
Thank you so much Joao for detailed answer. You are right, i think i should
write my own code. But since i don't have much experience in programming,
would you please introduce me some useful examples?
And(see below; our former conversations)
Best
Rose
On Wed, 12 Sep 2018, 20:04 João Henriques,
rompp, my system had not
integer charges, is it because of i ignore the polar groups and didn't
protonate carboxyl groups?
Best
On Wed, 29 Aug 2018, 22:46 Justin Lemkul, wrote:
>
>
> On 8/29/18 2:13 PM, Nick Johans wrote:
> > Thank you so much Iris.
> > want to sim
ture_1833992660]
>
> Iris Nira Smith | Postdoctoral Fellow | Genomic Medicine Institute
> Cleveland Clinic | 9500 Euclid Ave. / NE5-255 | Cleveland, OH 44195 |
> (216) 445-7885
>
>
>
>
> From: on behalf of
> Nick Johans
> Reply-To: "gmx-us...@gro
field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
What does it mean "protonated" ? How they add H when they have used AMBER
forcefield?
Would you please help me?
Best regards
On Wed, 29 Aug 2018, 19:50 Nick Johans, wrote:
> Hi,
>
&
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
Hi,
I deleted the pullf.xvg file unintentionally. Is there anyway to restore
and reproduce it from other outputs?
Best regards
-Nick
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maybe this is irrelative but i expeienced in pulling that when i decrease
dt from 2fs to 1fs i could make AA much closer to Sheet (0.1 nm)in
comparison with 2fs(max 0.4 nm). it's normal but these pulling runs were
crushed before(when dt=2fs) so i had had to decrease nsteps or decrease
pull_rate ,
and i have AA between sheet and wall.and it should get closer to sheet
during pulling. How should i set the initial place of amino acid? it should
have the minimum interaction with wall and sheet , am i right?
On Fri, Feb 2, 2018 at 7:14 PM, Rose wrote:
>
>
> Sent from my iPhone
>
> > On Feb 2,
Sorry, i think there is sth, maybe i've learnt wrong. let me draw it ;)
| = ZnS SHEET and@=Protein
conf0.gro
|
|
|<(Z)distance=1.76--->@
t=0
|
|
next time if dZ=0.5 so;
|
|
|<-(Z)distance=1.26>@
t=t1
|
|
next time if dZ=0.8 so;
|
|
|<-(Z)di
Hi, i,m a beginner. i us pdb2gmx or generating topology files.this is
aminoacid pdb file;
ATOM 1 N HIS 1 0.102 -0.143 0.000 1.00 0.00
N
ATOM 2 CA HIS 1 1.558 -0.029 0.000 1.00 0.00
C
ATOM 3 C HIS 1 1.986 1.419 0.000 1.00 0.00
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