Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Justin Lemkul 



On 8/29/18 2:34 PM, Nick Johans wrote:

Thank you dear justin. I'll read the paper. But  practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
  removed from insulin 43 residues. The C-terminal carboxyl groups and all
  the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
  Parameterized force field parameters for
  protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
I didn't protonate the molecule, so when i used grompp, my system had not
integer charges, is it because of i ignore the polar groups and didn't
protonate carboxyl groups?


No, the quoted passage means all amino acids were treated in their 
conjugate acid form (i.e. the dominant form at extremely low pH). This 
has nothing to do with a non-integer charge, simply that if you did not 
do the same thing, you're going to get protonation according to the 
dominant form at neutral pH. If you don't have an integer, you have a 
problem that pdb2gmx should have warned you about (long bonds => missing 
atoms, etc.)


-Justin


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 simulate a protwin interaction with nanotube. The question is

the

pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin

has

4 chain?


You need to read the paper associated with that crystal structure as
well as header information in the PDB file as to why this is. A crystal
complex is not necessarily the same as a functional complex.

-Justin


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:


Hi Nick,

I think the big question is what are you trying to simulate – what is

your

goal? It is critical that you now your protein (e.g. how was it
crystalized, any missing atoms, missing residues, hetero atoms,

ligands). I

think prior to building your system you should first understand your

goal

and get a stronger foundation on MDS as well as the forcefiled you

require

to model your system, this will help you better understand the flags for
each gmx command.

I would start with first reading the gromacs manual and re-reading the
reference paper associated with your PDB. Present your hypothesis and
goal(s) to your colleagues – this will help you formulate a
hypothesis-driven project.

Iris





[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_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...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp,

the

system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work

with

-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."


And how should protonate molecule in AMBER ff?

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,

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
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?


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Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Nick Johans 
Thank you dear justin. I'll read the paper. But  practically it is
mentioned that (for simulation) it has 51 residues which exactly equal to
A,B chain.
And i hope you answer the question about protonating " Residues B23-B30
were
 removed from insulin 43 residues. The C-terminal carboxyl groups and all
 the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
 Parameterized force field parameters for
 protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
I didn't protonate the molecule, so when i used grompp, 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 simulate a protwin interaction with nanotube. The question is
> the
> > pdb file structure. As i have not simulate protein before and i know that
> > insulin has 2 chains the question is that why in pdbcode(3e7y) insulin
> has
> > 4 chain?
> >
>
> You need to read the paper associated with that crystal structure as
> well as header information in the PDB file as to why this is. A crystal
> complex is not necessarily the same as a functional complex.
>
> -Justin
>
> > On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:
> >
> >> Hi Nick,
> >>
> >> I think the big question is what are you trying to simulate – what is
> your
> >> goal? It is critical that you now your protein (e.g. how was it
> >> crystalized, any missing atoms, missing residues, hetero atoms,
> ligands). I
> >> think prior to building your system you should first understand your
> goal
> >> and get a stronger foundation on MDS as well as the forcefiled you
> require
> >> to model your system, this will help you better understand the flags for
> >> each gmx command.
> >>
> >> I would start with first reading the gromacs manual and re-reading the
> >> reference paper associated with your PDB. Present your hypothesis and
> >> goal(s) to your colleagues – this will help you formulate a
> >> hypothesis-driven project.
> >>
> >> Iris
> >>
> >>
> >>
> >>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_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...@gromacs.org" 
> >> Date: Wednesday, August 29, 2018 at 11:36 AM
> >> To: "gmx-us...@gromacs.org" 
> >> Subject: [BULK][EXT] Re: [gmx-users] PDB code
> >>
> >> Sorry, i have just removed C,D chains by pymol and then started
> >> simulating(without adding any terminal or H,...)... but after grompp,
> the
> >> system had charges and were not integer. Is it because of i didn't add
> >> terminals? I use AMBER99SB forcefield and as you know it doesn't work
> with
> >> -ter but i have read paper which is said( that's my reference paper);
> >> " Residues B23-B30 were
> >> removed from insulin 43 residues. The C-terminal carboxyl groups and all
> >> the charged residues were set to be
> >> protonated to simulate the protein structures under acidic conditions.
> >> Parameterized force field parameters for
> >> protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
> >>
> > And how should protonate molecule in AMBER ff?
> >
> > 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,
> >>>
> >>> 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
> >>> should remove C,D chains, is there any tool to remove them standardly
> >>> ;)(not manually)?
> >>>
> >>> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> >>> starting simulation?
> >>>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
> >>
> https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org
> >
> >> before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
> >>
> https://protect-us.mimecast.com/s/-YXNCJ6Avkt55YjUvCgAi?domain=gromacs.org
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users<
> >>
> https://protect-us.mimecast.com/s/HUA1CKrBwlimmnRSGaanT?domain=maillist.sys.kth.se
> >
> >> or send a mail to gmx-users-requ...@gromacs.org.
> >>
> >>
> >> ===
> >>
> >>
>

Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Justin Lemkul 



On 8/29/18 2:13 PM, Nick Johans wrote:

Thank you so much Iris.
  want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4 chain?



You need to read the paper associated with that crystal structure as 
well as header information in the PDB file as to why this is. A crystal 
complex is not necessarily the same as a functional complex.


-Justin


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:


Hi Nick,

I think the big question is what are you trying to simulate – what is your
goal? It is critical that you now your protein (e.g. how was it
crystalized, any missing atoms, missing residues, hetero atoms, ligands). I
think prior to building your system you should first understand your goal
and get a stronger foundation on MDS as well as the forcefiled you require
to model your system, this will help you better understand the flags for
each gmx command.

I would start with first reading the gromacs manual and re-reading the
reference paper associated with your PDB. Present your hypothesis and
goal(s) to your colleagues – this will help you formulate a
hypothesis-driven project.

Iris



[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_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...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force field parameters for
protonated C-terminal carboxyl groups were used (Hong et al., 2012)."


And how should protonate molecule in AMBER ff?

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,

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
should remove C,D chains, is there any tool to remove them standardly
;)(not manually)?

How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
starting simulation?


--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org>
before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
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or send a mail to gmx-users-requ...@gromacs.org.


===


  Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country
by U.S. News & World Report (2017-2018). Visit us online at
http://www.clevelandclinic.org for a complete listing of our services,
staff and locations. Confidentiality Note: This message is intended for use
only by the individual or entity to which it is addressed and may contain
information that is privileged, confidential, and exempt from disclosure
under applicable law. If the reader of this message is not the intended
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Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Nick Johans 
Thank you so much Iris.
 want to simulate a protwin interaction with nanotube. The question is the
pdb file structure. As i have not simulate protein before and i know that
insulin has 2 chains the question is that why in pdbcode(3e7y) insulin has
4 chain?


On Wed, 29 Aug 2018, 22:00 Smith, Iris,  wrote:

> Hi Nick,
>
> I think the big question is what are you trying to simulate – what is your
> goal? It is critical that you now your protein (e.g. how was it
> crystalized, any missing atoms, missing residues, hetero atoms, ligands). I
> think prior to building your system you should first understand your goal
> and get a stronger foundation on MDS as well as the forcefiled you require
> to model your system, this will help you better understand the flags for
> each gmx command.
>
> I would start with first reading the gromacs manual and re-reading the
> reference paper associated with your PDB. Present your hypothesis and
> goal(s) to your colleagues – this will help you formulate a
> hypothesis-driven project.
>
> Iris
>
>
>
> [/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_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...@gromacs.org" 
> Date: Wednesday, August 29, 2018 at 11:36 AM
> To: "gmx-us...@gromacs.org" 
> Subject: [BULK][EXT] Re: [gmx-users] PDB code
>
> Sorry, i have just removed C,D chains by pymol and then started
> simulating(without adding any terminal or H,...)... but after grompp, the
> system had charges and were not integer. Is it because of i didn't add
> terminals? I use AMBER99SB forcefield and as you know it doesn't work with
> -ter but i have read paper which is said( that's my reference paper);
> " Residues B23-B30 were
> removed from insulin 43 residues. The C-terminal carboxyl groups and all
> the charged residues were set to be
> protonated to simulate the protein structures under acidic conditions.
> Parameterized force field parameters for
> protonated C-terminal carboxyl groups were used (Hong et al., 2012)."
>
And how should protonate molecule in AMBER ff?

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,
> >
> > 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
> > should remove C,D chains, is there any tool to remove them standardly
> > ;)(not manually)?
> >
> > How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> > starting simulation?
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List<
> https://protect-us.mimecast.com/s/TLbLCG6xpNtGGMziQt_Dy?domain=gromacs.org>
> before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
> https://protect-us.mimecast.com/s/-YXNCJ6Avkt55YjUvCgAi?domain=gromacs.org
> >
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users<
> https://protect-us.mimecast.com/s/HUA1CKrBwlimmnRSGaanT?domain=maillist.sys.kth.se>
> or send a mail to gmx-users-requ...@gromacs.org.
>
>
> ===
>
>
>  Please consider the environment before printing this e-mail
>
> Cleveland Clinic is currently ranked as the No. 2 hospital in the country
> by U.S. News & World Report (2017-2018). Visit us online at
> http://www.clevelandclinic.org for a complete listing of our services,
> staff and locations. Confidentiality Note: This message is intended for use
> only by the individual or entity to which it is addressed and may contain
> information that is privileged, confidential, and exempt from disclosure
> under applicable law. If the reader of this message is not the intended
> recipient or the employee or agent responsible for delivering the message
> to the intended recipient, you are hereby notified that any dissemination,
> distribution or copying of this communication is strictly prohibited. If
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> immediately and destroy the material in its entirety, whether electronic or
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> --
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>
> * Please search the archive at
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Re: [gmx-users] [BULK][EXT] Re: PDB code

2018-08-29 Thread Smith, Iris 
Hi Nick,

I think the big question is what are you trying to simulate – what is your 
goal? It is critical that you now your protein (e.g. how was it crystalized, 
any missing atoms, missing residues, hetero atoms, ligands). I think prior to 
building your system you should first understand your goal and get a stronger 
foundation on MDS as well as the forcefiled you require to model your system, 
this will help you better understand the flags for each gmx command.

I would start with first reading the gromacs manual and re-reading the 
reference paper associated with your PDB. Present your hypothesis and goal(s) 
to your colleagues – this will help you formulate a hypothesis-driven project.

Iris


[/Users/smithi4/Library/Containers/com.microsoft.Outlook/Data/Library/Caches/Signatures/signature_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...@gromacs.org" 
Date: Wednesday, August 29, 2018 at 11:36 AM
To: "gmx-us...@gromacs.org" 
Subject: [BULK][EXT] Re: [gmx-users] PDB code

Sorry, i have just removed C,D chains by pymol and then started
simulating(without adding any terminal or H,...)... but after grompp, the
system had charges and were not integer. Is it because of i didn't add
terminals? I use AMBER99SB forcefield and as you know it doesn't work with
-ter but i have read paper which is said( that's my reference paper);
" Residues B23-B30 were
removed from insulin 43 residues. The C-terminal carboxyl groups and all
the charged residues were set to be
protonated to simulate the protein structures under acidic conditions.
Parameterized force 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,
>
> 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
> should remove C,D chains, is there any tool to remove them standardly
> ;)(not manually)?
>
> How about Zn, Cl atoms there? Should i remove all nonbonded atoms when
> starting simulation?
>
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
 before posting!

* Can't post? Read 
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===


 Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as the No. 2 hospital in the country by 
U.S. News & World Report (2017-2018). Visit us online at 
http://www.clevelandclinic.org for a complete listing of our services, staff 
and locations. Confidentiality Note: This message is intended for use only by 
the individual or entity to which it is addressed and may contain information 
that is privileged, confidential, and exempt from disclosure under applicable 
law. If the reader of this message is not the intended recipient or the 
employee or agent responsible for delivering the message to the intended 
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communication in error, please contact the sender immediately and destroy the 
material in its entirety, whether electronic or hard copy. Thank you.
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