Re: [gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Rana Rehan Khalid]

Hi
I have ff of heme fe---o2  some one use it before these are amber heme ff
he use amber 99sb and this heme ff in his md  simulation  but he done his
work in amber. Can you guide me that how I can use this heme ff of amber in
combination with amber99sb  at number 6 position in gromacs

On Jun 14, 2017 4:55 PM, "Justin Lemkul"  wrote:



On 6/14/17 12:25 AM, Rana Rehan Khalid wrote:

> Hi
> I have read the chapter 5 of manual but i am confuse how can i add residue
> into heme atom of .rtp ff
> this is the coordinate due to which error come
>
> HETATM 1529  O01 HEM   187   3.996  19.101  70.594  0.00
> 0.00   O
>
> kindly guide me how i can make changes in the rtp file and .atp so that
> this error remove
> here is the heme rtp part of my selected ff where i can add O01 and also
> tell me these 4 column and these values and tell me which value i add for
> O01 like (FE FE 0.4 0 )
>

You should refer back to the manual if the contents of these files are not
clear.  You're seeking to introduce new parameters for an oxygen-bound form
of heme; this may require very complex parametrization work.  Modifying an
.rtp file is trivial; it's just text.  Putting realistic parameters into it
is a whole other matter.  Check the literature for any existing efforts to
avoid duplicated work.

-Justin


[ HEME ]
>   [ atoms ]
> FEFE 0.4 0
> NANR-0.1 0
> NBNR-0.1 0
> NCNR-0.1 0
> NDNR-0.1 0
>CHA C-0.1 1
>HHAHC 0.1 1
>C1A C 0.0 2
>C2A C 0.0 2
>C3A C 0.0 2
>C4A C 0.0 2
>CMA   CH3 0.0 3
>CAA   CH2 0.0 4
>CBA   CH2 0.0 4
>CGA C 0.27000 5
>O1AOM-0.63500 5
>O2AOM-0.63500 5
>CHB C-0.1 6
>HHBHC 0.1 6
>C1B C 0.0 7
>C2B C 0.0 7
>C3B C 0.0 7
>C4B C 0.0 7
>CMB   CH3 0.0 8
>CAB   CR1 0.0 9
>CBB   CH2 0.0 9
>CHC C-0.110
>HHCHC 0.110
>C1C C 0.011
>C2C C 0.011
>C3C C 0.011
>C4C C 0.011
>CMC   CH3 0.012
>CAC   CR1 0.013
>CBC   CH2 0.013
>CHD C-0.114
>HHDHC 0.114
>C1D C 0.015
>C2D C 0.015
>C3D C 0.015
>C4D C 0.015
>CMD   CH3 0.016
>CAD   CH2 0.017
>CBD   CH2 0.017
>CGD C 0.2700018
>O1DOM-0.6350018
>O2DOM-0.6350018
>
> thanks
>
>
-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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[gmx-users] How i can use amber heme ff in gromacs

[Rana Rehan Khalid]

I have force field for Heme FeO2 that are amber .prm file how can i use
it in combination of Amber99 ff. because when i run the simulation with
amber99 this error come Residue 'HEM' not found in residue topology
database
 while now i have specific ff for fe---o2 bond heme file that is .prm file
kindly guide me how i use this amber .prm file  in gromacs in combination
with amber99
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Re: [gmx-users] Regarding change in residue name during conversion from pdb 2 gro file

[Mark Abraham]

Hi,

That's a non-standard pdb file (see ATOM
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html) so not too
surprising. I'd complain at whoever generated it, and change the name of
the rtp entry.

Mark

On Mon, 26 Jun 2017 18:01 Dilip H N  wrote:

> Hello all,
> I have a .pdb file with residue name as DMAM , so while i try to convert
> the .pdb file into .gro file by the command :-
> gmx editconf -f abc.pdb -o abc.gro
> the .gro file is generated but the residue name is being changed to
> DMA...which during the simulation mixture setup gives errors as residue not
> found it residue topology...
> So how do i avoid this residue name getting changed during the conversion
> from .pdb file to .gro file...??
>
> Thank you
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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[gmx-users] gmx distance

[Pandya, Akash]

Hi all,

I'm trying to calculate the distance between two groups using the following 
command line:


gmx distance -f md_0_1.xtc -s md_0_1.tpr -oav distance.xvg -select `com of 
group "1" plus com of group "14"`


Group 1 is my protein and Group 14 is my ligand. There is an error message that 
shows up:

Inconsistency in user input:
Selection 'Protein' does not evaluate into an even number of positions (there
are 6617 positions)

I'm not sure how to solve this problem. Does anyone have a solution?
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[gmx-users] Regarding change in residue name during conversion from pdb 2 gro file

[Dilip H N]

Hello all,
I have a .pdb file with residue name as DMAM , so while i try to convert
the .pdb file into .gro file by the command :-
gmx editconf -f abc.pdb -o abc.gro
the .gro file is generated but the residue name is being changed to
DMA...which during the simulation mixture setup gives errors as residue not
found it residue topology...
So how do i avoid this residue name getting changed during the conversion
from .pdb file to .gro file...??

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] CG MD

[Alex Mathew]

>though most atomistic properties can be studied by rebuilding the
atomistic coordinates from the CG. Various methods exist to >do this.

Could you please provide a link to any material or paper for this.
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Re: [gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I have encountered the following warning when I used the following code to 
minimize my protein-ligand system when the interaction potential energy between 
the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp

Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is 
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


I suppose this error is due to setting couple-intramol = no. When it is set to 
yes, the warning vanishes.

But, this is my desired setting since, I do not intend to scale the intra 
molecular interactions even though the ligand is a peptide. Is it reasonable to 
ignore the warning. If not , how can it affect my resulting structure ? And are 
all such interaction "ignored for the rest of the simulation" ?

Apologies for the previous incomplete mail.

Best Regards,

Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Wednesday, June 14, 2017 4:50:58 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I aspire to derive energy-minimum structures when the interaction potential 
> energy between the protein and the ligand are multiplied by 0.9, 0.8, 
> 0.7,..., 0.2, 0.1.
> 
> I presume the following Free Energy minimization code mentioned in gromacs 
> tutorial may do the trick. I would appreciate if you could please verify if 
> it produces my intended result.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 

Possibly, but the outcomes may be unphysical.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I have encountered the following error when I used the 

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 
Error:

Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is 
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size


Best Regards,

Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Wednesday, June 14, 2017 4:50:58 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I aspire to derive energy-minimum structures when the interaction potential 
> energy between the protein and the ligand are multiplied by 0.9, 0.8, 
> 0.7,..., 0.2, 0.1.
> 
> I presume the following Free Energy minimization code mentioned in gromacs 
> tutorial may do the trick. I would appreciate if you could please verify if 
> it produces my intended result.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 

Possibly, but the outcomes may be unphysical.

-Justin

-- 
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Fwd: Relative free energy perturbation

[Hannes Loeffler]

On Mon, 26 Jun 2017 12:25:19 +0200
Davide Bonanni  wrote:

> 1) Can I perform the calculation in a single step with soft core
> potential enabled? I mean, is it correct to transform directly the
> hydrogen into a chlorine instead of using 2 topologys and 2
> complexes, where in the first step I transform the hydrogen into
> dummy atom, and in the second I transform the dummy atom into
> chlorine.

Technically speaking you can perfectly do that but in practice it can
be much more efficient to directly and linearly transform one atom type
into another (single topology approach).  There is no need for a
softcore potential in this case.  Those would only be activated for
atoms that either appear or disappear i.e. atoms with zero vdW
parameters.  The input and topology files from FEsetup should be all
you need.


> 2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
> x-tutorials/free_energy/index.html), I have to perform every step of
> molecular dynamics at every Lambda value, is that right?

Yes, you will need to do a simulation for every and each lambda step.


> 3) I run a test minimization step (mdp file attached) of my complex
> at the last "init-lambda-state", 15 in my case. Looking at the .trr
> output file I can see that the bond between the carbon and the
> hydrogen which should be trasformed is longer than a normal C-H bond,
> but the atom is still recognized as hydrogen (picture
> "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ;
> blue -> init-lambda-state = 15). I was wondering if this is what I am
> supposed to see, so if gromacs is considering the state B of my
> system where I have chlorine bound to carbon instead hydrogen.

What does "recognized as hydrogen" mean?  I suspect that what you are
referring to is the output of some visualisation program because you
instructed it to interpret that particular atom to be a hydrogen.

What you need to expect to see is that a C-H bond is transformed into a
C-Cl bond and accordingly the bond length increases.
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[gmx-users] negative reaction coordinate during pulling

[edesantis]

dear all,

I am studing the affinity between an antibody and a peptide; I am 
intrested in the evaluation of the PMF using gmx wham after the umbrella 
sampling technique.



During the pulling steps, the absolute value of the reaction coordinates 
increases, while its sign is negative,

It could be a problem for the code??

thank you in advance
best regards
Emiliano



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Emiliano De Santis
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[gmx-users] How to convert AMBER trajectory to Gromacs trajectory

[Saikat Pal]

Dear all,


I have converted Amber trajectory (.mdcrd ) to Gromacs trajectory (.trr) using 
Amber 14 cpptraj. But Now I want to convert .trr to .xtc format. I have used 
this command:  trjconv -s output1.pdb -f qdna-1.trr -o md_0_1.xtc -pbc none -ur 
compact
It shows:
Last frame -1 time    0.000   

Setting output precision to 0.001 (nm)

WARNING no output, last frame read at t=0


gcq#131: "You Fill Your Space So Sweet" (F. Apple)


output1.pdb=generated by cpptraj


please help me out. I am not much familiar with gromacs.I am using gromacs 
4.6.7.
Thanks and regards,
Saikat
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[gmx-users] Fwd: Relative free energy perturbation

[Davide Bonanni]

Hi,

I am trying to perform an alchemical free energy perturbation with gromacs,
since I am approaching this technique for the first time. So, it would be
so nice if you could help me to clarify some doubt.

I have built my system, which is composed of 1 protein, 2 cofactors, and 1
ligand that should changes from state A to B.
I used FESetup to make the topology for my ligand. The change I want to
apply to my molecule is just the transformation of a hydrogen into
chlorine, so I do not have dummy atoms involved. This is the only string
that changes from state A to B in my ligand topology:

[Atoms]
; Nr type resnm atom cgnr   chargemass  typeB  chargeB   massB
   30 h4 1 LIG H30  30   0.158051 1.0080   cl -0.078297   35.4500

So, I have the complex.gro and complex.top, I made some minimization tests
and everything seems good. I have some doubts on the procedure I'm supposed
to follow to perform FEP calculation. Some questions:

1) Can I perform the calculation in a single step with soft core potential
enabled? I mean, is it correct to transform directly the hydrogen into a
chlorine instead of using 2 topologys and 2 complexes, where in the first
step I transform the hydrogen into dummy atom, and in the second I
transform the dummy atom into chlorine. Using soft core potential I can
perform any kind of transformation in single step, or are there some cases
where I need to use different procedures?

2) Referring to BevanLab Tutorial 6: Free Energy Calculation (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm
x-tutorials/free_energy/index.html), I have to perform every step of
molecular dynamics at every Lambda value, is that right?

3) I run a test minimization step (mdp file attached) of my complex at the
last "init-lambda-state", 15 in my case. Looking at the .trr output file I
can see that the bond between the carbon and the hydrogen which should be
trasformed is longer than a normal C-H bond, but the atom is still
recognized as hydrogen (picture "http://tinypic.com/r/2wp11dh/9": purple ->
init-lambda-state = 0 ; blue -> init-lambda-state = 15). I was wondering if
this is what I am supposed to see, so if gromacs is considering the state B
of my system where I have chlorine bound to carbon instead hydrogen.

I am apologize if my questions are technically incorrect. As I said it is
the first time I'm approaching to free energy perturbation and every kind
of help and suggestion is really appreciated.

Thank you very much in advance.

Best regards,

Davide Bonanni

--
Davide Bonanni, PhD student
Dept. Science and Drug Technology
University of Turin (UniTO) - Italy
Mobile +39 3409726272 <+39%20340%20972%206272>
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Re: [gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script

[Nikhil Maroli]

Hi,
Read the header file of the script or use python X.py will give the
usage warning/information.
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Re: [gmx-users] Regarding conversion of charmm ff to gromacs by cgenff_charmm2gmx.py script

[Mark Abraham]

Hi,

This is a list for GROMACS related questions. This looks like a support
problem for cgenff. Please read their FAQs and contact them. Note also
their message that you should probably use a python 2.7 version.

Mark

On Mon, Jun 26, 2017 at 7:16 AM Dilip H N  wrote:

> Hello all,
> I uploaded a molecule in mol.2 format in cgenff and thn i got the output
> file in .str format. and now i am converting the .str which is in charmm
> format to gromacs format using the script cgenff_charmm2gmx.py by the
> following command as:-
>
> python cgenff_charmm2gmx.py abc abc.str abc.mol2 charmm26-nov2016.ff
>
> but i am getting the following errors..
>
> NOTE1: Code tested with python 2.7.3. Your version:
> NOTE2: Please be sure to use the same version of CGenFF in your simulations
> that was used during parameter generation:
> Traceback (most recent call last):
>   File "cgenff_charmm2gmx.py", line 777, in 
> check_versions(rtp_name,ffdir + "/forcefield.doc")
>   File "cgenff_charmm2gmx.py", line 60, in check_versions
> f = open(ffdoc_filename, 'r')
> FileNotFoundError: [Errno 2] No such file or directory: 'charmm26
> nov2016.ff/forcefield.doc'
>
> How to solve this error..??
>
> Thank you...
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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Re: [gmx-users] dssp installation using cygwin

[Mark Abraham]

Hi,

Same as with UNIX. Download the windows binary and teach gmx do_dssp where
it is.

Mark

On Mon, Jun 26, 2017 at 10:26 AM Neha Gupta  wrote:

> Hi gromacs users,
>
>  I am using gromacs in windows  through cygwin
>
> How to install dssp through cygwin?
>
> Can anyone help?
>
> Thanks,
> Neha
> --
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> posting!
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Re: [gmx-users] CGMD with cut-off Verlet?

[Peter Kroon]

For posterity, you can find a sample mdp file here
http://cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp
and the corresponding paper here http://dx.doi.org/10.1016/j.cpc.2015.09.014


Peter


On 23-06-17 19:15, Mark Abraham wrote:
> Hi,
>
> And follow the advice of the Martini authors for using the Verlet scheme
> with their forcefield.
>
> Mark
>
> On Fri, 23 Jun 2017 17:20 Justin Lemkul  wrote:
>
>>
>> On 6/23/17 11:08 AM, Alex Mathew wrote:
>>> Dear all,
>>>
>>> While running CGMD in GPU i got this error
>>>
>>> OpenMP threads have been requested with cut-off scheme Group, but these
>> are
>>> only supported with cut-off scheme Verlet
>>>
>>> Here can i change the cut-off scheme to Verlet ?
>> Amazingly enough:
>>
>> cutoff-scheme = Verlet
>>
>> in the .mdp file :)
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
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>> posting!
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>>


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[gmx-users] dssp installation using cygwin

[Neha Gupta]

Hi gromacs users,

 I am using gromacs in windows  through cygwin

How to install dssp through cygwin?

Can anyone help?

Thanks,
Neha
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Re: [gmx-users] MD simulation at different pH

[Anand Balupuri]

Dear João,

Thank you for your suggestions.

Regards,
Anand

On Mon, Jun 26, 2017 at 3:47 PM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> Hi!
>
> You technically can't perform constant-pH simulations with a regular,
> straight out of the box GROMACS distribution. You can change the residue
> protonation states to mimic the "pH" you're interested in simulating, but
> keep in mind that these will be fixed during the entire simulation, i.e.
> there are no (de)protonation events.
>
> For actual constant-pH methods start by reading:
>
> http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
>
> There are other MD simulation packages natively distributed with the
> ability to perform constant-pH simulations (e.g. AMBER).
>
> Best regards,
> João
>
>
> On Mon, Jun 26, 2017 at 3:14 AM, Anand Balupuri <
> anandbalupuri.ni...@gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > I want to perform MD simulations at different pH using Gromacs 5.0. How
> can
> > I carry out such simulations? Any suggestions?
> >
> > Many thanks,
> > Anand
> > --
> > Gromacs Users mailing list
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> >
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Re: [gmx-users] MD simulation at different pH

[João Henriques]

Hi!

You technically can't perform constant-pH simulations with a regular,
straight out of the box GROMACS distribution. You can change the residue
protonation states to mimic the "pH" you're interested in simulating, but
keep in mind that these will be fixed during the entire simulation, i.e.
there are no (de)protonation events.

For actual constant-pH methods start by reading:

http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

There are other MD simulation packages natively distributed with the
ability to perform constant-pH simulations (e.g. AMBER).

Best regards,
João


On Mon, Jun 26, 2017 at 3:14 AM, Anand Balupuri <
anandbalupuri.ni...@gmail.com> wrote:

> Dear Gromacs users,
>
> I want to perform MD simulations at different pH using Gromacs 5.0. How can
> I carry out such simulations? Any suggestions?
>
> Many thanks,
> Anand
> --
> Gromacs Users mailing list
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> Support/Mailing_Lists/GMX-Users_List before posting!
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