Re: [gmx-users] OpenMosix and Gromacs

[Ansgar Esztermann]

On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote:
> 
> I wonder if someone has some experience with Gromacs and OpenMosix. Has 
> someone tried recently to run Gromacs in parallel with an OpenMosix 
> cluster? I have read some messages about that on the mailing-list but 

I have not tried that; but I do have some experience with OpenMosix
development, and I would not expect that combination to work well.
oM copes very well with dynamic loads since it distributed
processes on the fly, but Gromacs is more likely to generate a static
load that does not change at all during the simulation run.
However, some spurious migrations will likely take place even during a
static load scenario, taking away quite some time (on the order of seconds). 

Moreover, oM does not in itself provide any inter-process communication,
so MPI is needed anyway. There might be a problem with shared memory 
(which is not supported by oM).

Finally, most syscalls are very slow under oM since they are executed on 
the home node. This pertains especially to file operations, which go
through the network unbuffered.


All in all, oM was written to solve a problem that usually does not
occur when running programs like Gromacs, so there seem to be many
potential problems but little benefit from combining those two.


A.
-- 
Ansgar Esztermann
Researcher & Sysadmin
http://www.mpibpc.mpg.de/groups/grubmueller/start/people/aeszter/index.shtml


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Re: [gmx-users] OpenMosix and Gromacs

[Erik Lindahl]

Hi,

On Jul 2, 2007, at 11:15 AM, Ansgar Esztermann wrote:


On Fri, Jun 29, 2007 at 03:49:01PM -0600, Nicolas Sapay wrote:


I wonder if someone has some experience with Gromacs and  
OpenMosix. Has

someone tried recently to run Gromacs in parallel with an OpenMosix
cluster? I have read some messages about that on the mailing-list but


I have not tried that; but I do have some experience with OpenMosix
development, and I would not expect that combination to work well.
oM copes very well with dynamic loads since it distributed
processes on the fly, but Gromacs is more likely to generate a static
load that does not change at all during the simulation run.
However, some spurious migrations will likely take place even during a
static load scenario, taking away quite some time (on the order of  
seconds).


Moreover, oM does not in itself provide any inter-process  
communication,

so MPI is needed anyway. There might be a problem with shared memory
(which is not supported by oM).

Finally, most syscalls are very slow under oM since they are  
executed on

the home node. This pertains especially to file operations, which go
through the network unbuffered.


All in all, oM was written to solve a problem that usually does not
occur when running programs like Gromacs, so there seem to be many
potential problems but little benefit from combining those two.



At least in the "old days", Mosix did not support migration sockets,  
i.e. processes doing communication. Not sure if that has been solved,  
but since Gromacs just uses MPI calls for communication we never have  
any knowledge about node names, IP numbers etc - that's entirely up  
to the MPI library.


Thus, if an MPI implementation works fine on Mosix Gromacs will too,  
and the CVS 3.99 branch will load balance beautifully. If MPI doesn't  
work there's nothing we can do.


Cheers,

Erik
 
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[gmx-users] Dismantling the methyl group

[Jussi Lehtola]

Hi,



I've run into problems with simulating a methanol - water system. My
purpose is to do an electronic structure calculation for configurations
generated with Gromacs, however the thing is that Gromacs handles the
methyl group as a single unit whereas I need the coordinates of the
carbon and of the three hydrogens for the quantum mechanic computations.

Is there any simple way to put the hydrogens in place using Gromacs, or
do I need to program a way myself?
-- 
Mr. Jussi Lehtola
Research Assistant
Division of Theoretical Physics / Division of High Energy Physics
IT services

Department of Physical Sciences
University of Helsinki


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Re: [gmx-users] Dismantling the methyl group

[Tsjerk Wassenaar]

Hi Jussi,

Gromacs only handles the methyl as a single particle if you tell it
to, i.e. by taking a united atom force field like GROMOS. You can use
OPLS/Amber in stead. Of course you can add the hydrogens based on an
ideal geometry for each frame, but I think you'll miss part of the
points of generating structures for electronic calculations in that
case.

Cheers,

Tsjerk

On 7/2/07, Jussi Lehtola <[EMAIL PROTECTED]> wrote:

Hi,



I've run into problems with simulating a methanol - water system. My
purpose is to do an electronic structure calculation for configurations
generated with Gromacs, however the thing is that Gromacs handles the
methyl group as a single unit whereas I need the coordinates of the
carbon and of the three hydrogens for the quantum mechanic computations.

Is there any simple way to put the hydrogens in place using Gromacs, or
do I need to program a way myself?
--
Mr. Jussi Lehtola
Research Assistant
Division of Theoretical Physics / Division of High Energy Physics
IT services

Department of Physical Sciences
University of Helsinki


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Dismantling the methyl group

[Erik Marklund]

Hi,

You should use an all-atom force field. I assume you're using one of  
the Gromos force fields, which is of united-atom type.


/Erik

2 jul 2007 kl. 12.27 skrev Jussi Lehtola:


Hi,



I've run into problems with simulating a methanol - water system. My
purpose is to do an electronic structure calculation for  
configurations

generated with Gromacs, however the thing is that Gromacs handles the
methyl group as a single unit whereas I need the coordinates of the
carbon and of the three hydrogens for the quantum mechanic  
computations.


Is there any simple way to put the hydrogens in place using  
Gromacs, or

do I need to program a way myself?
--
Mr. Jussi Lehtola
Research Assistant
Division of Theoretical Physics / Division of High Energy Physics
IT services

Department of Physical Sciences
University of Helsinki


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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED]   http://xray.bmc.uu.se/molbiophys


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[gmx-users] S-S Bonds

[Roberto Marchese]

Dear GROMACS Users,
I want to do MD of insulin monomer (first two chain of 4ins.pdb).  
When I convert with pdb2gmx, the software find only one ss bond (the  
only inside the same chain). I have resolved this problem doing a  
first conversion pdb->gro, then gro->pdb end in the final conversion  
pdb->gro the software find the all three ss bond, and number the  
residues of the two chain like one.


But now there is the big problem, when I do a two step minimization  
(for bad contacts) the two chain go away, like no ss bonds exist.
Whit VMD I can see that all the S atoms is on one chain (the first,  
whit have the internal SS bond). Then there are two CYS with two S  
atoms and two (on the other chain) with no S atom.
I have cecked the topology file, and the bond between CB and S, and S- 
S  are all correct.


I think that the problem is inside the two chain configuration, but I  
haven't explanation for the CYS without S.


Thanks
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Re: [gmx-users] S-S Bonds

[Tsjerk Wassenaar]

Hi Roberto,


I want to do MD of insulin monomer (first two chain of 4ins.pdb). When I
convert with pdb2gmx, the software find only one ss bond (the only inside
the same chain). I have resolved this problem doing a first conversion
pdb->gro, then gro->pdb end in the final conversion pdb->gro the software
find the all three ss bond, and number the residues of the two chain like
one.


You should check my post from this morning on another thread about SS
bonds (hint: pdb2gmx option -merge).
Also, your pdb -> gro -> pdb -> gro conversions don't change anything.
You also can't infer from the structure in a viewer whether you have
an SS bond listed in the topology. The topology is a different thing.



But now there is the big problem, when I do a two step minimization (for bad
contacts) the two chain go away, like no ss bonds exist.


Because there is no SS bond...; see above.


Whit VMD I can see that all the S atoms is on one chain (the first, whit
have the internal SS bond). Then there are two CYS with two S atoms and two
(on the other chain) with no S atom.
I have cecked the topology file, and the bond between CB and S, and S-S  are
all correct.

I think that the problem is inside the two chain configuration, but I
haven't explanation for the CYS without S.



I haven't got a clue on your 'CYS without S', but you are right that
the other part has to do with having two chains...

Hope it helps,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Dismantling the methyl group

[Jussi Lehtola]

Hi again,



thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have
a .gro file (& al) for methanol using OPLS or another all-hydrogen force
field? I tried running pdb2gmx on the tutorial .pdb files, but it failed
with the error

Fatal error:
Atom Me1 in residue MET 1 not found in rtp entry with 17 atoms
 while sorting atoms
-- 
Mr. Jussi Lehtola
Research Assistant
Division of Theoretical Physics / Division of High Energy Physics
IT services

Department of Physical Sciences
University of Helsinki


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Re: [gmx-users] Dismantling the methyl group

[David van der Spoel]

Jussi Lehtola wrote:

Hi again,



thanks to Tsjerk and Erik for a quick reply. Would anyone happen to have
a .gro file (& al) for methanol using OPLS or another all-hydrogen force
field? I tried running pdb2gmx on the tutorial .pdb files, but it failed
with the error

Fatal error:
Atom Me1 in residue MET 1 not found in rtp entry with 17 atoms
 while sorting atoms

chapter 5.

pdb2gmx only works on proteins.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] Dismantling the methyl group

[Erik Marklund]

2 jul 2007 kl. 14.32 skrev David van der Spoel:


Jussi Lehtola wrote:

Hi again,
thanks to Tsjerk and Erik for a quick reply. Would anyone happen  
to have
a .gro file (& al) for methanol using OPLS or another all-hydrogen  
force
field? I tried running pdb2gmx on the tutorial .pdb files, but it  
failed

with the error
Fatal error:
Atom Me1 in residue MET 1 not found in rtp entry with 17 atoms
 while sorting atoms

chapter 5.

pdb2gmx only works on proteins.



(And nucleic acids)
/Erik


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala  
University.

Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED]   http://xray.bmc.uu.se/molbiophys


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[gmx-users] trajconv

[ann rose]

Hi all

I am new to Gromacs: I am simulating pure polymer (22 monomers and 16 linear
chains) in vaccum and i have a few questions regarding the trjconv command.

I run a NPT simulation for 500 picosecond and when i see the output (.gro)
file in vmd i found some holes my simulation box.
I mean 2 or 3 chains were away from the center position of the box where
other chains were residing.

so i thought of performing a NVT simulation follwed by BD for my system to
be equillibriated.

1. Will that help in the  purpose of equillibriation?

so, for that i wanted to center all the polymer chains inside the box and
performed the trjconv program.
But I wonder
2.Which ouput file from my 500 ps simulation (.xtc or .gro )  shall i use to
perform the trjconv and which options (-pbc nojump, -pbc whole) shall I
specify inorder to achieve my goal?
or
3.the holes that i have mentioned before are accpetable or not?
4.is it can be the problem with VMD visualisation?

out of interest i performed the trjconv with .gro file as follows

trjconv -f abc.gro -s abc.tpr -pbc nojump -o output.gro

but when i viewed the output.gro in vmd i found most of my chains were
broken.

5.which file i have to give as input and what makes the difference (.xtc
file or .gro file?)

then i tried wth .xtc file as input as follows

trjconv -f abc.xtc -s abc.tpr -pbc nojump -o output.gro

this time it was not found to be broken.

Waiting for any suggestions


Thanking in advance
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Re: [gmx-users] trajconv

[Tsjerk Wassenaar]

Hi Ann,


I run a NPT simulation for 500 picosecond and when i see the output (.gro)
file in vmd i found some holes my simulation box.
I mean 2 or 3 chains were away from the center position of the box where
other chains were residing.

so i thought of performing a NVT simulation follwed by BD for my system to
be equillibriated.

1. Will that help in the  purpose of equillibriation?


No. This has nothing to do with equilibration but is due to periodic
boundary conditions. Check chapter 3 of the manual, the wiki and the
archives of this list to learn more.



so, for that i wanted to center all the polymer chains inside the box and
performed the trjconv program.
But I wonder
2.Which ouput file from my 500 ps simulation (.xtc or .gro )  shall i use to
perform the trjconv and which options (-pbc nojump, -pbc whole) shall I
specify inorder to achieve my goal?
or


For centering you don't need any if the -pbc options. But when using
-pbc nojump you have to make sure that the reference structure is
close to the initial structure in the trajectory you want to reset, as
I explained in more detail last week or the week before.


3.the holes that i have mentioned before are accpetable or not?


Not a problem... PBC.


4.is it can be the problem with VMD visualisation?


Since it's not a problem it can't be a problem with visualization ;)
(Though it can pose a problem when visualization is the aim, then you
need to use -pbc nojump or inbox)



out of interest i performed the trjconv with .gro file as follows

trjconv -f abc.gro -s abc.tpr -pbc nojump -o output.gro

but when i viewed the output.gro in vmd i found most of my chains were
broken.


...which is due to a too large shift between the reference structure
(your final structure) and the first structure in your trajectory.



5.which file i have to give as input and what makes the difference (.xtc
file or .gro file?)


Either take the .tpr or take the .pdb file you started from (after
addition of hydrogens and such; the atoms must match).



then i tried wth .xtc file as input as follows

trjconv -f abc.xtc -s abc.tpr -pbc nojump -o output.gro

this time it was not found to be broken.


...which proves my point.


Waiting for any suggestions



Hope it helps,

Tsjerk

--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Applying constant force between two atoms

[SeungPyo Hong]

Dear gmx-users,



I want to apply constant force between two atoms within a protein.

But unfortunately I cannot find how to apply constant force.

Would anybody talk me how to do it?



Thanks,



Seungpyo
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Re: [gmx-users] Applying constant force between two atoms

[Mark Abraham]

> Dear gmx-users,
>
>
>
> I want to apply constant force between two atoms within a protein.
>
> But unfortunately I cannot find how to apply constant force.
>
> Would anybody talk me how to do it?

Probably not, but if you read Chapters 3-5 of the manual, you will see
some ideas that are probably more suitable for whatever your underlying
objective is.

Mark

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Re: [gmx-users] pdb2gmx not recognizing disulfides

[Russell Green]

Hmm...well the thing is, I just need a .tpr file (which I was getting with
pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to xtc
format. The simulation is already complete, I'm just converting it, but of
course the atoms from the tpr need to match those of the trajectory. So
should I still be doing something different other than my idea to change the
residue names of the .itp files, as mentioned previously? Sorry for some of
my ignorance, I'm still new with much of this. Thanks for all the
suggestions and input!

Thanks,
Russell Green


On 7/2/07, David van der Spoel <[EMAIL PROTECTED]> wrote:


Russell Green wrote:
>
>I did try changing the bond length but it wouldn't catch all the
> disulfides. I do have multiple chains but I don't believe they should be
> merged. My current work around is to just leave the disulfide residues
> named CYX according to the amber format and then change them to CYS2 in
> the .itp files for the corresponding .top file. This way pdb2gmx doesn't
> protonate the disulfide residues and the charges for CYS2 are
> maintained. If anyone thinks this is not a good idea, please tell me.
>
it's still not clear what you want to do. if your CYS are at 0.2 nm
distance pdb2gmx will make the bonds. if they are not, why would you
want them to form? anyway, if you want to do that, please follow
Tsjerk's advice below.


> Thanks,
> Russell
>
> On 7/2/07, *Tsjerk Wassenaar* <[EMAIL PROTECTED]
> > wrote:
>
> Hi Russel,
>
> You never mentioned the distance between the
> 'sulphurs-that-wouldn't-connect'. Are they beyond the range normal
for
> disulphide bonds? If so, you could try to add an additional entry in
> the specbond.dat file with a different bond length. Maybe you'll
have
> to change the residue name first, although it could work without (I
> don't know whether pdb2gmx properly handles multiple multiple
> distances for the same atom pair, but it's easy to find out).
> Another thing you never mentioned is whether the cysteines are from
> one chain or from different chains. In the latter case, you have to
> use the option -merge with pdb2gmx. pdb2gmx will not usually make
> bonds between different chains.
>
>

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] pdb2gmx not recognizing disulfides

[David van der Spoel]

Russell Green wrote:
Hmm...well the thing is, I just need a .tpr file (which I was getting 
with pdb2gmx followed by grompp) so I can convert an amber pdb 
trajectory to xtc format. The simulation is already complete, I'm just 
converting it, but of course the atoms from the tpr need to match those 
of the trajectory. So should I still be doing something different other 
than my idea to change the residue names of the .itp files, as mentioned 
previously? Sorry for some of my ignorance, I'm still new with much of 
this. Thanks for all the suggestions and input!
 
Thanks,

Russell Green



for this purpose you could also use a pdb file.


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] pdb2gmx not recognizing disulfides

[Mark Abraham]

> Hmm...well the thing is, I just need a .tpr file (which I was getting with
> pdb2gmx followed by grompp) so I can convert an amber pdb trajectory to
> xtc
> format. The simulation is already complete, I'm just converting it, but of
> course the atoms from the tpr need to match those of the trajectory. So
> should I still be doing something different other than my idea to change
> the
> residue names of the .itp files, as mentioned previously? Sorry for some
> of
> my ignorance, I'm still new with much of this. Thanks for all the
> suggestions and input!

So take a frame from the trajectory which you know has sensible disulfide
bond lengths, embed that in a structure file using some Amber tool, and
use that as your input to pdb2gmx.

Mark

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Re: [gmx-users] pdb2gmx not recognizing disulfides

[Yang Ye]

If you are using trjconv, a gro or pdb can be fed to -s option. tpr is 
not necessary.


Regards,
Yang Ye

On 7/2/2007 10:01 PM, Russell Green wrote:
Hmm...well the thing is, I just need a .tpr file (which I was getting 
with pdb2gmx followed by grompp) so I can convert an amber pdb 
trajectory to xtc format. The simulation is already complete, I'm just 
converting it, but of course the atoms from the tpr need to match 
those of the trajectory. So should I still be doing something 
different other than my idea to change the residue names of the .itp 
files, as mentioned previously? Sorry for some of my ignorance, I'm 
still new with much of this. Thanks for all the suggestions and input!
 
Thanks,

Russell Green

 
On 7/2/07, *David van der Spoel* <[EMAIL PROTECTED] 
> wrote:


Russell Green wrote:
>
>I did try changing the bond length but it wouldn't catch all the
> disulfides. I do have multiple chains but I don't believe they
should be
> merged. My current work around is to just leave the disulfide
residues
> named CYX according to the amber format and then change them to
CYS2 in
> the .itp files for the corresponding .top file. This way pdb2gmx
doesn't
> protonate the disulfide residues and the charges for CYS2 are
> maintained. If anyone thinks this is not a good idea, please
tell me.
>
it's still not clear what you want to do. if your CYS are at 0.2 nm
distance pdb2gmx will make the bonds. if they are not, why would you
want them to form? anyway, if you want to do that, please follow
Tsjerk's advice below.


> Thanks,
> Russell
>
> On 7/2/07, *Tsjerk Wassenaar* <[EMAIL PROTECTED]

> mailto:[EMAIL PROTECTED]>>> wrote:
>
> Hi Russel,
>
> You never mentioned the distance between the
> 'sulphurs-that-wouldn't-connect'. Are they beyond the range
normal for
> disulphide bonds? If so, you could try to add an additional
entry in
> the specbond.dat file with a different bond length. Maybe
you'll have
> to change the residue name first, although it could work
without (I
> don't know whether pdb2gmx properly handles multiple multiple
> distances for the same atom pair, but it's easy to find out).
> Another thing you never mentioned is whether the cysteines
are from
> one chain or from different chains. In the latter case, you
have to
> use the option -merge with pdb2gmx. pdb2gmx will not usually
make
> bonds between different chains.
>
>

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax:
+4618511755.
[EMAIL PROTECTED]
[EMAIL PROTECTED]
   http://folding.bmc.uu.se
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Re: [gmx-users] Dismantling the methyl group

[Yang Ye]

Can you figure out which type of atom is this Me1?

Regards,
Yang Ye

On 7/2/2007 8:45 PM, Erik Marklund wrote:


2 jul 2007 kl. 14.32 skrev David van der Spoel:


Jussi Lehtola wrote:

Hi again,
thanks to Tsjerk and Erik for a quick reply. Would anyone happen to 
have
a .gro file (& al) for methanol using OPLS or another all-hydrogen 
force
field? I tried running pdb2gmx on the tutorial .pdb files, but it 
failed

with the error
Fatal error:
Atom Me1 in residue MET 1 not found in rtp entry with 17 atoms
 while sorting atoms

chapter 5.

pdb2gmx only works on proteins.



(And nucleic acids)
/Erik


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: 
+4618511755.

[EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
[EMAIL PROTECTED]http://xray.bmc.uu.se/molbiophys


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Re: [gmx-users] Dismantling the methyl group

[Jussi Lehtola]

On Mon, 2007-07-02 at 23:08 +0800, Yang Ye wrote:
> Can you figure out which type of atom is this Me1?
> 
> Regards,
> Yang Ye

It is the methyl group, CH_3.
-- 
Mr. Jussi Lehtola
Research Assistant
Division of Theoretical Physics / Division of High Energy Physics
IT services

Department of Physical Sciences
University of Helsinki



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Re: [gmx-users] [Fwd: How simulate two peptides in a box?]

[gurpreet singh]

Hello Gromacs users:


I am running a  dimeric protein simulation on Gromacs 3.3 using the force
filed G43a1.


For initially minimizing the hydrogen i did some small minimization and
equilibration in the vacuum by maintaining the restraints
then i added ions and water but in the very first minimization i m getting
the following error


1-4 interaction between 1 and 9 at distance 8.454 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,


In the log file i am getting :

4 inconsistent shifts check your topology

following is my input file :

title   = 1min in water
define  = -DPOSRES
integrator  = steep
dt  = 0.001
constraints = none
nsteps  = 500
nstlist = 10
rcoulomb= 1
rlist   = 1
rvdw= 1.4
ns_type = grid
coulombtype = PME
pbc = xyz
gen_vel = no
fourierspacing  = 0.12
pme_order   = 6
ewald_rtol  = 1e-5
optimize_fft= yes
comm_mode   = angular
emtol   = 100.0
emstep  = 0.01


after adding the ions i have modified the topology file,
please tell me what is the exact reason for this error or what are the
other things i should check in relation to the  error

With regards
Thanks

On 7/2/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:


Hi Fufeng Liu,

I guess you ran pdb2gmx on the two peptides, where both peptides had
the same chain identifiers. In that case, pdb2gmx will assume that
it's one molecule and connect them. Use chain identifiers to indicate
the different peptides, or build topologies first on separate files
and combine the peptides later.

Cheers,

Tsjerk

On 7/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Please keep requests for help on the list. That way they're archived for
> others to use, and other people can raise points of interest.
>
> The last sentence here
>
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
> is my suggestion for you :-) Probably, you have only one [molecule]
> statement for your two molecules, and by chance you included it first so
> that there was no error message from grompp. If you don't understand why
> this is a problem, find the relevant section of Chapter 5 of the manual
-
> or read the whole lot of that chapter! :-)
>
> Mark
>
>  Original Message

> Subject: How simulate two peptides in a box?
> From:[EMAIL PROTECTED]
> Date:Sun, July 1, 2007 11:09 pm
> To:  [EMAIL PROTECTED]
>
--
>
> Dear Mark:
>  I'm a graduate student at Tianjin University. I want to simulate
two
> peptides
> in a box using GROMACS software? I followed your suggestion
>
> {set up your topologies (suggest one molecule in each of two .itp files)
> #include them in the .top file, pick a starting configuration for both
of
> them in the same structure file, solvate, minimize.}
>
> But when I minimized the system, I got the information ¡±1-4 interaction
> between 83 and 85 at distance 1.862 which is larger than the 1-4 table
> size 1.000 nm¡±. I checked the topology and found that atom 83 belong to
> one peptide and the atom 85 the other peptide. That¡¯s to say the two
> peptides were considered as a peptide. Can you tell me how to do?  I'd
be
> very happy and grateful if you could tell me how to do it.
> Looking forward to your reply.
>  Best regards.
>  Fufeng Liu
>
>
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] pdb2gmx not recognizing disulfides

[Russell Green]

Thanks for the tip. I didn't think to try it. But if I plan to do any
electrostatics I still need the tpr file right? So I would need to produce a
top file. Mark, you mentioned making the S-S bonds by hand.


You still won't get them bonded with this procedure... you need a .top
file with S-S bonds, and you get that by producing one by hand or using
pdb2gmx.


Could you or anyone else point me in the right direction to do this?

Again, thanks for all the help and insight.

Russell Green
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[gmx-users] What is the box type of output files?

[Lam Nguyen Sy]

Dear all,

I am new to Gromacs, and I am trying to simulate my
systems with octahedral box type (the option I used
for editconf was "-bt octahedral"). 
I need to know what type of box that Gromacs put the
output systems in, because I am trying to do some
translations on some molecules that are outside the
box to put them inside, so that I can correctly
compute the number of contacts.
When using VMD to visualize some output .gro or .pdb
files, I just saw a rectangular box. Furthermore, it
is said on page 12 of the GROMACS User Manual version
3.3 that "Even when simulating using a triclinic box,
GROMACS always puts the particles in a brick shaped
volume, for efficiency reason" and "So from the output
trajectory it might seem like the simulation was done
in a rectangular box." I am not clear on this point. 
There is a series of numbers at the end of my .gro
files:
4.12763   3.89157   3.37019   0.0   0.0  
1.37588   0.0  -1.37588   1.94578
I guess they are the components of the box vectors.

What type of box does GROMACS usually put an output
system in? And in the case of my systems, what is the
type of box containing them in the output files?

Any help would be very useful. Thank you in advanced.

Nguyen Sy Lam


 

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Re: [gmx-users] What is the box type of output files?

[Yang Ye]

On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote:

Dear all,

I am new to Gromacs, and I am trying to simulate my
systems with octahedral box type (the option I used
for editconf was "-bt octahedral"). 
I need to know what type of box that Gromacs put the

output systems in, because I am trying to do some
translations on some molecules that are outside the
box to put them inside, so that I can correctly
compute the number of contacts.
When using VMD to visualize some output .gro or .pdb
files, I just saw a rectangular box. Furthermore, it
is said on page 12 of the GROMACS User Manual version
3.3 that "Even when simulating using a triclinic box,
GROMACS always puts the particles in a brick shaped
volume, for efficiency reason" and "So from the output
trajectory it might seem like the simulation was done
in a rectangular box." I am not clear on this point. 
There is a series of numbers at the end of my .gro

files:
4.12763   3.89157   3.37019   0.0   0.0  
1.37588   0.0  -1.37588   1.94578

I guess they are the components of the box vectors.
  
Gromacs always output the type of box you have choosen. Because VMD 
doesn't support octahedral-type of box, it simply read the first three 
numbers and set them for x-, y-, and z-dimensions. You need to use 
"trjconv -ur compact -pbc atom" to convert your trajectory as well as 
your gro or pdb file to get them correctly displayed.

What type of box does GROMACS usually put an output
system in? And in the case of my systems, what is the
type of box containing them in the output files?

Any help would be very useful. Thank you in advanced.

Nguyen Sy Lam


 

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[gmx-users] which tpr?

[Terry Nelson]

Hello all,

Because of the limitations in run time, my simulations have broken into
three parts: one.trr, two.trr, and three.trr. Each run has its corresponding
tpr file. The original tpr file (minimization step) was start.tpr. Now using
trjconv for three.trr which tpr file I need to type after -s option?

trjconv -f three.trr -s start.tpr 

I am aware that the topology (information in the starting top file) will
remain intact during simulation. I am wondering whether commands like
trjconv read anything more than topology information  (MD parameters, etc)
from the -s option? In other words, in the above example replacing
start.tprwith
three.tpr will not change the outcome?


Cheers,
Terry
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Re: [gmx-users] which tpr?

[David van der Spoel]

Terry Nelson wrote:

Hello all,
 
Because of the limitations in run time, my simulations have broken into 
three parts: one.trr, two.trr, and three.trr. Each run has its 
corresponding tpr file. The original tpr file (minimization step) was 
start.tpr. Now using trjconv for three.trr which tpr file I need to type 
after -s option?
 
trjconv -f three.trr -s start.tpr 
 
I am aware that the topology (information in the starting top file) will 
remain intact during simulation. I am wondering whether commands like 
trjconv read anything more than topology information  (MD parameters, 
etc) from the -s option? In other words, in the above example replacing 
start.tpr with three.tpr will not change the outcome? 


no.

for some analysis tools it may but not here. you could have tred it out 
of course, and compared the results using gmxcheck.


Cheers,
Terry




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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] What is the box type of output files?

[Lam Nguyen Sy]

Thank you very much, it is very helpful for me.

nslam

Yang Ye <[EMAIL PROTECTED]> wrote: On 7/3/2007 2:24 AM, Lam Nguyen Sy wrote:
> Dear all,
>
> I am new to Gromacs, and I am trying to simulate my
> systems with octahedral box type (the option I used
> for editconf was "-bt octahedral"). 
> I need to know what type of box that Gromacs put the
> output systems in, because I am trying to do some
> translations on some molecules that are outside the
> box to put them inside, so that I can correctly
> compute the number of contacts.
> When using VMD to visualize some output .gro or .pdb
> files, I just saw a rectangular box. Furthermore, it
> is said on page 12 of the GROMACS User Manual version
> 3.3 that "Even when simulating using a triclinic box,
> GROMACS always puts the particles in a brick shaped
> volume, for efficiency reason" and "So from the output
> trajectory it might seem like the simulation was done
> in a rectangular box." I am not clear on this point. 
> There is a series of numbers at the end of my .gro
> files:
> 4.12763   3.89157   3.37019   0.0   0.0  
> 1.37588   0.0  -1.37588   1.94578
> I guess they are the components of the box vectors.
>   
Gromacs always output the type of box you have choosen. Because VMD 
doesn't support octahedral-type of box, it simply read the first three 
numbers and set them for x-, y-, and z-dimensions. You need to use 
"trjconv -ur compact -pbc atom" to convert your trajectory as well as 
your gro or pdb file to get them correctly displayed.
> What type of box does GROMACS usually put an output
> system in? And in the case of my systems, what is the
> type of box containing them in the output files?
>
> Any help would be very useful. Thank you in advanced.
>
> Nguyen Sy Lam
>
>
>  
> 
> Finding fabulous fares is fun.  
> Let Yahoo! FareChase search your favorite travel sites to find flight and 
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Re: [gmx-users] pdb2gmx not recognizing disulfides

[Mark Abraham]

> Thanks for the tip. I didn't think to try it. But if I plan to do any
> electrostatics I still need the tpr file right? So I would need to produce
> a
> top file. Mark, you mentioned making the S-S bonds by hand.

You can see that trjconv doesn't really need a .tpr because trjconv -h
shows you that -s allows any structure file type as input. This is a
general GROMACS phenomenon.

>>You still won't get them bonded with this procedure... you need a .top
>>file with S-S bonds, and you get that by producing one by hand or using
>>pdb2gmx.
>
> Could you or anyone else point me in the right direction to do this?

I'm a bit hamstrung because I don't know
a) why you are trying to make S-S bonds from a structure that has sulfurs
more than 2A apart
b) where this structure came from
c) whether you have tried the second procedure I suggested in the email
you quote http://www.gromacs.org/pipermail/gmx-users/2007-July/028337.html
d) whether you have tried the other suggestion I made
http://www.gromacs.org/pipermail/gmx-users/2007-July/028356.html

Making the topology by hand requires you to read chapter five of the
manual thoroughly and then go through a working topology with the manual
at hand so  that you understand all the bits. Only then could you hope to
make a S-S topology by hand, and then you'll probably run into hassles
with things breaking when you try to minimize with it. Much easier will be
c) or d) above.

Mark

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Re: [gmx-users] which tpr?

[Mark Abraham]

> Hello all,
>
> Because of the limitations in run time, my simulations have broken into
> three parts: one.trr, two.trr, and three.trr. Each run has its
> corresponding
> tpr file. The original tpr file (minimization step) was start.tpr. Now
> using
> trjconv for three.trr which tpr file I need to type after -s option?
>
> trjconv -f three.trr -s start.tpr 
>
> I am aware that the topology (information in the starting top file) will
> remain intact during simulation. I am wondering whether commands like
> trjconv read anything more than topology information  (MD parameters, etc)
> from the -s option? In other words, in the above example replacing
> start.tprwith
> three.tpr will not change the outcome?

trjconv just needs any old structure file. You can see this if you follow
my suggestion at the top of this post
http://www.gromacs.org/pipermail/gmx-users/2007-July/028367.html

Mark

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Re: [gmx-users] Applying constant force between two atoms

[SeungPyo Hong]

Thank you for paying attention.
Maybe I have to study much more about Gromacs. ^^;

Seungpyo

On 7/2/07, Mark Abraham <[EMAIL PROTECTED]> wrote:


> Dear gmx-users,
>
>
>
> I want to apply constant force between two atoms within a protein.
>
> But unfortunately I cannot find how to apply constant force.
>
> Would anybody talk me how to do it?

Probably not, but if you read Chapters 3-5 of the manual, you will see
some ideas that are probably more suitable for whatever your underlying
objective is.

Mark

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Re: [gmx-users] [Fwd: How simulate two peptides in a box?]

[Mark Abraham]

>  Hello Gromacs users:

Please don't reply to another user's question with a change of topic and
not change the subject line of your email. Not doing this means the people
who might know the answer for you have no idea in advance what you're
going to be asking, and might not bother reading. Best is to start with a
new email, not a reply, and to use your subject line sensibly.

> I am running a  dimeric protein simulation on Gromacs 3.3 using the force
> filed G43a1.
>
>
> For initially minimizing the hydrogen i did some small minimization and
> equilibration in the vacuum by maintaining the restraints
> then i added ions and water but in the very first minimization i m getting
> the following error

If you want to keep your credibility, when people have already made a
suggestion about how to solve your problem, such as I did here
http://www.gromacs.org/pipermail/gmx-users/2007-June/028301.html, when you
post the same problem, you should say what happened when you tried their
suggestion. They didn't suggest it for their own entertainment.

Look at the minimization "trajectory" and see where things are breaking.
Have a look at your topology there, read chapter five thoroughly.

Mark

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[gmx-users] g_wham and PMF problem

[Sudha Mani Karra]

Hey All,
   I am trying to use g_wham command to compute PMF.Can anyone please let
me know how to use that command?
When I try giving the input files sequentially like

g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,

there is an error message saying, that it is not a valid input file format.

I have seen in the previous mailing lists that people have faced the same
kind of error. I hope I get a reply from them as they would have solved
this.

Thanks in advance.
S.Karra.
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Re: [gmx-users] g_wham and PMF problem

[Mark Abraham]

> Hey All,
> I am trying to use g_wham command to compute PMF.Can anyone please let
> me know how to use that command?

Well there's g_wham -h and the section on WHAMin the manual...

> When I try giving the input files sequentially like
>
> g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,
>
>  there is an error message saying, that it is not a valid input file
> format.

Please be specific about the error message and the file that caused it.
Computers are precise, and you should be also in describing their
responses to your inputs.

Mark

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[gmx-users] How to get ligand top file for oplsaa?

[Rui Li]

Dear all,
I have a ligand molecule, and I want to get its opls all-atom force field 
topology
file. How can I get it?
I don't know how to establish the atom types and the charge of the ligand.
Any reply will be appreciated.

sincerely
Rui Li


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Re: [gmx-users] which tpr?

[Tsjerk Wassenaar]

Hey :)

Errm, trjconv does read coordinates, so when using -fit or -pbc
nojump, the results will depend on the structure file used.

Tsjerk

On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:

> Hello all,
>
> Because of the limitations in run time, my simulations have broken into
> three parts: one.trr, two.trr, and three.trr. Each run has its
> corresponding
> tpr file. The original tpr file (minimization step) was start.tpr. Now
> using
> trjconv for three.trr which tpr file I need to type after -s option?
>
> trjconv -f three.trr -s start.tpr 
>
> I am aware that the topology (information in the starting top file) will
> remain intact during simulation. I am wondering whether commands like
> trjconv read anything more than topology information  (MD parameters, etc)
> from the -s option? In other words, in the above example replacing
> start.tprwith
> three.tpr will not change the outcome?

trjconv just needs any old structure file. You can see this if you follow
my suggestion at the top of this post
http://www.gromacs.org/pipermail/gmx-users/2007-July/028367.html

Mark

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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] How to get ligand top file for oplsaa?

[Tsjerk Wassenaar]

Hi Rui Li,

See http://wiki.gromacs.org/index.php/Parameterization

Tsjerk

On 7/3/07, Rui Li <[EMAIL PROTECTED]> wrote:

Dear all,
I have a ligand molecule, and I want to get its opls all-atom force field 
topology
file. How can I get it?
I don't know how to establish the atom types and the charge of the ligand.
Any reply will be appreciated.

sincerely
Rui Li


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] g_wham and PMF problem

[Sudha Mani Karra]

Hey Mark,
 Appreciate your immediate response.You can find the input and the
error below:
g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo pull5.pdo

   :-)  g_wham  (-:

Option Filename  Type Description

 -opmf.xvg  Output   xvgr/xmgr file
-hist pull1.pdo.xvg  Output   xvgr/xmgr file

 Option   Type  Value  Description
--
 -[no]h   bool no  Print help info and quit
  -niceint  0  Set the nicelevel
 -[no]w   bool no  View output xvg, xpm, eps and pdb files
  -[no]xvgr   boolyes  Add specific codes (legends etc.) in the output
   xvg files for the xmgrace program
   -min   real  0  Minimum coordinate in profile
   -max   real  0  Maximum coordinate in profile
  -binsint100  Number of bins in profile
  -[no]prof   boolyes  Only calculate min and max
  -temp   real298  Temperature
  -[no]flip   bool no  Combine halves of profile
   -tol   real   0.01  Tolerance

Opening file pull2.pdo.

gunzip: stdin: not in gzip format
---
Program g_wham, VERSION 3.3.1
Source code file: gmx_wham.c, line: 90

Fatal error:
This does not appear to be a valid pdo file
---

Thanks ,
S.K



On 7/2/07, Mark Abraham <[EMAIL PROTECTED]> wrote:


> Hey All,
> I am trying to use g_wham command to compute PMF.Can anyone please
let
> me know how to use that command?

Well there's g_wham -h and the section on WHAMin the manual...

> When I try giving the input files sequentially like
>
> g_wham -o PMF.XVG -hist pull1.pdo pull2.pdo pull3.pdo,
>
>  there is an error message saying, that it is not a valid input file
> format.

Please be specific about the error message and the file that caused it.
Computers are precise, and you should be also in describing their
responses to your inputs.

Mark

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Re: [gmx-users] which tpr?

[Mark Abraham]

> Hey :)
>
> Errm, trjconv does read coordinates, so when using -fit or -pbc
> nojump, the results will depend on the structure file used.
>
> Tsjerk
>
> On 7/3/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>> trjconv just needs any old structure file. You can see this if you
>> follow
>> my suggestion at the top of this post
>> http://www.gromacs.org/pipermail/gmx-users/2007-July/028367.html

Ermm yes. I should have said "trjconv just needs a file with the structure
you want in any old structure format"

Mark

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Re: [gmx-users] g_wham and PMF problem

[Mark Abraham]

> Hey Mark,
>   Appreciate your immediate response.You can find the input and
> the
> error below:
> g_wham -o pmf.xvg -hist pull1.pdo pull2.pdo pull3.pdo pull4.pdo pull5.pdo

g_wham -h suggests that -hist won't accept multiple input files. Only a
few GROMACS utilities will do magic concatenation for you. Have a look at
the file format and see what you need to do with a text editor or command
line tools.

> Opening file pull2.pdo.
>
> gunzip: stdin: not in gzip format
> ---
> Program g_wham, VERSION 3.3.1
> Source code file: gmx_wham.c, line: 90
>
> Fatal error:
> This does not appear to be a valid pdo file
> ---

Does g_wham -o pmf.xvg -hist pull1.pdo work?

Mark

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