Hi DeepaK,
You should be aware that excess protons are not floating around freely
among a bunch of H2O. Whatever reasoning along this line is physically
meaningless (including thinking of a mixture of H3O+, H2O, OH-). This is
the realm of QM.
Cheers,
Tsjerk
On Thu, Oct 10, 2013 at 8:05 AM, De
Dear GMxers,
I want to simulate the proton transfer reaction in bulk water using
gromacs.I am not aware how to add proton using genion.Is it possible to add
excess protons like other ions.I could not find proton in ions.itp.
If anybody can guide me about the same.
Thanks
DeepaK Ojha
School Of Ch
On 10/9/13 4:09 PM, Sainitin Donakonda wrote:
What functional significance does it have, if any? --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand
Do you observe hydrogen bonds with the ligand?
What is the residue? -- *Glutam
Is that residue in a loop?
Gianluca
On Wed, 9 Oct 2013, Sainitin Donakonda wrote:
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite
What functional significance does it have, if any? --- According to my
knowledge this reside is present in binding site.. and forms some hydrogen
bonds with ligand
What is the residue? -- *Glutamic Acid*
What did you measure - RMSF of the whole residue, just the backbone, just
C-alpha, etc? --*
On 10/9/13 3:29 PM, Sainitin Donakonda wrote:
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but o
Hi all,
I recently performed MD simulation of protein - ligand complex..and
analyzed its trajectory using RMSF tool in gromacs.
This analysis revealed particular residue in binding site of protein showed
quite high fluctuation around 0.30 nm but other residues were in range of
0.15 to 0.20
Can a
On 10/9/13 1:26 PM, Roland Schulz wrote:
Hi Justin,
are you guys planning anything to make pdb2gmx understand the CHARMM patch
residues? We have some python scripts which generate new residues based on
the patch residues, which allows us to simulate branched molecules (e.g.
glycosylation or li
OK thank you four kind response. And also thank you and the CHARMM team for
this geat job.
Stephane
---
On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote:
> Hello Justin,
>
> Two quick questions, here
>
> - Since the lipid charmm36 parameters for lipids are already available in the
>
Hi Justin,
are you guys planning anything to make pdb2gmx understand the CHARMM patch
residues? We have some python scripts which generate new residues based on
the patch residues, which allows us to simulate branched molecules (e.g.
glycosylation or lignin). But that approach is very suboptimal a
On 10/9/13 9:09 AM, Atila Petrosian wrote:
Dear gromacs usres
I am doing simulation of lipid bilayer.
I did 2 steps: 1) energy minimization, 2) equilibration.
Before production run, I want to monitor dimensions of the simulation cell
to test the stability of the simulation.
On the other han
On 10/9/13 11:28 AM, ABEL Stephane 175950 wrote:
Hello Justin,
Two quick questions, here
- Since the lipid charmm36 parameters for lipids are already available in the
gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas
Piggot. Does it means that these files are co
Hello Justin,
Two quick questions, here
- Since the lipid charmm36 parameters for lipids are already available in the
gromacs format on the GROMACS website (charmm36.ff_4.5.4_ref.tgz) from thomas
Piggot. Does it means that these files are considered as deprecated and all the
users are invit
And ACPYPE does (besides several others improvements)
Alan
On 9 October 2013 15:24, xiao wrote:
> Hi Alan,
>
> Thank you very much! The problem is solved. The reason is that amb2gmx
> cannot distinguish the proper and improper dihedrals.
>
> Best wishes
>
> Fugui
>
>
>
>
> At 2013-10-09 21:58:
Hi Alan,
Thank you very much! The problem is solved. The reason is that amb2gmx cannot
distinguish the proper and improper dihedrals.
Best wishes
Fugui
At 2013-10-09 21:58:29,Alan wrote:
>Hi, try ACPYPE.
>
>Alan
>
>
>On 9 October 2013 14:07, xiao wrote:
>
>> Dear all,
>>
>> I am doing
Hi,
you can use g_energy, and then select X-box and Y-box in the prompt.
Bests,
Baptiste
2013/10/9 Atila Petrosian
> Dear gromacs usres
>
> I am doing simulation of lipid bilayer.
>
> I did 2 steps: 1) energy minimization, 2) equilibration.
>
> Before production run, I want to monitor dimens
Hi, try ACPYPE.
Alan
On 9 October 2013 14:07, xiao wrote:
> Dear all,
>
> I am doing membrane protein simulation by using amber force field. The
> lipid force field parameters are from the lipid11.dat from Amber. Firstly,
> i got the xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to
Dear gromacs usres
I am doing simulation of lipid bilayer.
I did 2 steps: 1) energy minimization, 2) equilibration.
Before production run, I want to monitor dimensions of the simulation cell
to test the stability of the simulation.
On the other hands, I want to plot dimensions of the simulation
Dear all,
I am doing membrane protein simulation by using amber force field. The lipid
force field parameters are from the lipid11.dat from Amber. Firstly, i got the
xx.prmtop and xx.prmcrd files, and then i used amb2gmx.pl to convert the
xx.prmtop and xx.prmcrd files into gromacs files xx.top
On 10/9/13 7:55 AM, CHEN Pan wrote:
Dear Justin,
Thanks for you information.
I have a small query on the residue name in the "charmm36.ff" folder. Is
there any document illustrating for the corresponding full name of residues
in the ".rtp" file.
As you have illustrated in the file "forcefield.
On 10/9/13 7:54 AM, rajat desikan wrote:
Thank you, Justin.
I am particularly interested in the lipid simulations. Can you upload the
final results on dropbox? Sorry for the trouble...I intend to simulate a
membrane-protein system using charmm36. I will let you know how that goes.
I will send
On 10/9/13 7:55 AM, CHEN Pan wrote:
Dear Justin,
Thanks for you information.
I have a small query on the residue name in the "charmm36.ff" folder. Is
there any document illustrating for the corresponding full name of residues
in the ".rtp" file.
As you have illustrated in the file "forcefield.
Hello,
I have read somewhere in the list that I cannot do pressure coupling
without pbc.
What I essentially need is a box with impermeable walls, that get smaller
as the simulation proceeds.
I do anisotropic pressure coupling with two impermeable walls (in xy axis)
for another simulation, and it
Dear Gromacs Users,
I am trying to look for some references regarding the SMD. I found one
which tells about logarithmically dependency between the Rupture force
(maximum pulling force) obtained from SMD and the pulling rate. Just
wondering whether you are aware (or tested) the dependency between
Dear Justin,
Thanks for you information.
I have a small query on the residue name in the "charmm36.ff" folder. Is
there any document illustrating for the corresponding full name of residues
in the ".rtp" file.
As you have illustrated in the file "forcefield.doc", the parameters for
some carbohydra
Thank you, Justin.
I am particularly interested in the lipid simulations. Can you upload the
final results on dropbox? Sorry for the trouble...I intend to simulate a
membrane-protein system using charmm36. I will let you know how that goes.
Thanks.
On Wed, Oct 9, 2013 at 5:20 PM, Justin Lemkul w
On 10/9/13 6:42 AM, Mass wrote:
Hi Justin
Thanks for your answer but I could not solve the problem, sorry
Can you tell me how can I fix this part? the highlighted part is your answer
I google it and found this on ubuntu forum but I followed it and still I am
getting error
up vote
0
down vote
On 10/9/13 7:03 AM, rajat desikan wrote:
Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
list of the test systems that you used? Thanks again.
We tested everything, at least in terms of representative examples. Single
amino acids, full proteins in vacuo, single n
Superb stuff, Justin. Thank you so much. Is it asking too much for a brief
list of the test systems that you used? Thanks again.
On Wed, Oct 9, 2013 at 1:46 AM, Justin Lemkul wrote:
>
> All,
>
> I am pleased to announce the immediate availability of the latest CHARMM36
> force field in GROMACS
Great! Many thanks Justin, and the CHARMM team!
Mark
On Tue, Oct 8, 2013 at 10:16 PM, Justin Lemkul wrote:
>
> All,
>
> I am pleased to announce the immediate availability of the latest CHARMM36
> force field in GROMACS format. You can obtain the archive from our lab's
> website at
> http://
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