Make index of water mediated hydrogens and DNA bases so that DNA bases are
in separate group and water mediated hydrogens in separate group in drop
down menu
On Thu, May 9, 2019, 11:54 AM wrote:
> Dear all
> I want to determine the water mediated hydrogen between DNA bases and
> small molecule.
niversity of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of paul buscemi
Sent: Sunday, January 6, 2019 12:41:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx hbon
Thank you. But it just adjusts the cut-off between atoms not the number of
hydrogen bonds in a given distance above the surface (or in the box). would
you please help me?
Best
On Sun, Jan 6, 2019 at 9:12 PM paul buscemi wrote:
> Use VMD/extensions/hydrogen bonds
>
> > On Jan 6, 2019, at 11:01 A
Use VMD/extensions/hydrogen bonds
> On Jan 6, 2019, at 11:01 AM, rose rahmani wrote:
>
> hi,
>
> I want to know the number of hydrogen bonds of amino acid with water in
> different distances above surface. for example in first 0.2nm, in second
> 0.2 nm(0.2-0.4 nm) above surface. how can i do it
On 4/13/18 2:22 AM, rose rahmani wrote:
Hi,
I have 2 questions, but please consider them 2 distinct questions and are
not related.
I did umbrella sapmling and calculate the PMF.
Now i I want to calculate number of hydrogen bonds for amino acid in its
initial distance(far from surface) and bind
work.
-Justin
Nilesh
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: Tuesday, April 10, 2018 6:45:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond
On 4/10/18 6:43 PM, Dhumal, Nilesh wrote:
I tried, didn&#
toms.
-Justin
> Nilesh
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on behalf of Justin
> Lemkul
> Sent: Tuesday, April 10, 2018 6:39:37 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] GMX hbond
>
&g
ilesh
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Justin Lemkul
Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond
On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
Hello Gromacs users,
ustin Lemkul
Sent: Tuesday, April 10, 2018 6:39:37 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] GMX hbond
On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
> Hello Gromacs users,
>
>
> I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION
> 5.1.4. I did fo
On 4/10/18 5:51 PM, Dhumal, Nilesh wrote:
Hello Gromacs users,
I am calculating hydrogen bond life time using gmx hbond in Groamcs VERSION
5.1.4. I did following steps
mx hbond -f traj.trr -s md.tpr -n index.ndx -ac
Reading file md.tpr, VERSION 5.1.4 (single precision)
Specify 2 groups to
Hi Negar,
Correct, the -dist option doesn’t do what you want it to. I cannot come up with
a recipe for how to do this, but I suspect multiple rounds of gmx select and
gmx hbond might do the trick.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodo
On 8/6/17 4:21 PM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Hi justin
Thank you for your replyingBut you said in this tuturial, in order to ha
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have
tc_groups = protein non-protein , it is bes
On 8/4/17 11:13 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i ne
Hi,
A quick glance at the code suggests Justin is right. You should be able to
inspect the output of gmx hbond and see that in fact -e means that many
fewer trajectory frames are being read.
Mark
On Tue, May 2, 2017 at 2:56 AM Justin Lemkul wrote:
>
>
> On 5/1/17 10:15 AM, Marcelo Depólo wrote
On 5/1/17 10:15 AM, Marcelo Depólo wrote:
Hi!
I am running ACF calculations in gmx hbond tool in 5.0.7 version.
When running:
gmx hbond -s mol.tpr -f mol.xtc -tu ns -b 0 -e 10 -ac acf_0-10ns.xvg
and
gmx hbond -s mol.tpr -f mol.xtc -b 0 -e 1 -ac acf_0-10ns.xvg
The results given for t
Thanks Erik, It helped.
Cheers
On Sat, Apr 15, 2017 at 9:30 AM, Erik Marklund
wrote:
> Dear Moshen,
>
> I doubt the difference in versions will cause any problems in this case.
>
> The second column is ill-described. It contains the number of pairs within
> 0.3 nm that don’t fulfil the angle cr
Dear Moshen,
I doubt the difference in versions will cause any problems in this case.
The second column is ill-described. It contains the number of pairs within 0.3
nm that don’t fulfil the angle criterion.
Kind regards,
Erik
__
Erik Marklund, PhD, Ma
Hi,
Not as of yet I’m afraid.
Erik
> On 3 May 2016, at 08:16, Nash, Anthony wrote:
>
>
> Hi all,
>
> Can gmx hbond accept user specified atoms for the donors (default OH and
> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
> this in the -help text.
>
> I have a post
On 5/3/16 5:21 PM, Nash, Anthony wrote:
Thanks Justin,
I’ll give that a try. I assume this approach would still require the .trr
to be converted to a .gro file, and then the customised names
‘search-replaced’ with the respective ‘fake’ names?
No. Names are read from the reference coordina
Thanks Justin,
I’ll give that a try. I assume this approach would still require the .trr
to be converted to a .gro file, and then the customised names
‘search-replaced’ with the respective ‘fake’ names?
Thanks
Anthony
On 03/05/2016 16:22, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
be
On 5/3/16 9:16 AM, Nash, Anthony wrote:
Hi all,
Can gmx hbond accept user specified atoms for the donors (default OH and
NH) and acceptor (default O and N)? I don¹t seem to find any mention of
this in the -help text.
It's hard-coded in the source, so it's rather inflexible.
I have a post
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