[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

Dear All
During researching Internet, I found justin and Anirban's tutorial
about embedding protein
in lipid membrane. It was useful and I appreciate them but I had one
question. as I understood, I should make some changes to protein pdb file
( 1r2h for Ex)
 before using it in  pdb2gmx command or the GROMACS can't
keep on and will be died with a fatal error ( something like adding cope
to the ends of the protein ). could
somebody please tell me what should I do ? by the way I found out that
Justin's
tutorial do something with xleap amber on the pdb file.
Please tell me how specifically I should revise my protein pdb file.

best regards
Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran

-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

Dear All
During researching Internet, I found justin and Anirban's tutorial
about embedding protein
in lipid membrane. It was useful and I appreciate them but I had one
question. as I understood, I should make some changes to protein pdb file
( 1r2h for Ex)
 before using it in  pdb2gmx command or the GROMACS can't
keep on and will be died with a fatal error ( something like adding cope
to the ends of the protein ). could
somebody please tell me what should I do ? by the way I found out that
Justin's
tutorial do something with xleap amber on the pdb file.
Please tell me how specifically I should revise my protein pdb file.

best regards
Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran






�

-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom:
0.1in; line-height: 120%; }a:link {  }


Hi Catarina


Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1 protein into DPPC lipid bilayer� which I already
downloaded it from rcsb.com.� when I tried to use pdb2gmx� via
"gmx pdb2gmx -f 2rh1.pdb -o 2rh1_processed.gro -ignh -ter -water
spc", it says :




�


Select start terminus type for ASP-29

�0: NH3+

�1: NH2

�2: None

2

Start terminus ASP-29: None

Select end terminus type for LEU-342

�0: COO-

�1: COOH

�2: None

2

End terminus LEU-342: None

---

Program gmx, VERSION 5.0.5

Source code file:
/home/ali/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1091



Fatal error:

There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

---


I found a similar question in which Justin replied it as below :


You haven't added caps onto the input protein, you should expect to
get this error. In the tutorial, I build ACE and NH2 groups onto the
peptide to neutralize the termini. Since you haven't done this type
of modification, pdb2gmx will die because you have incomplete amides at
the ends of the chain. The "None" terminus instructs pdb2gmx to
not build additional H (in the case of NH2 or NH3+ termini) or O(H) (for
COO- and COOH). It doesn't make any chemical sense to use
"None" for non-capped protein chains.


I don't grasp what specifically Justin meant to say. Could anyone 
one
please help me ? How should I naturalized the termini ?

best regards

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran




�

�

-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

Hi Catarina


Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1 protein into DPPC lipid bilayer� which I already
downloaded it from rcsb.com.� when I tried to use pdb2gmx� via
"gmx pdb2gmx -f 2rh1.pdb -o 2rh1_processed.gro -ignh -ter -water
spc", it says :




�


Select start terminus type for ASP-29

�0: NH3+

�1: NH2

�2: None

2

Start terminus ASP-29: None

Select end terminus type for LEU-342

�0: COO-

�1: COOH

�2: None

2

End terminus LEU-342: None

---

Program gmx, VERSION 5.0.5

Source code file:
/home/ali/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1091



Fatal error:

There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

---


I found a similar question in which Justin replied it as below :


You haven't added caps onto the input protein, you should expect to
get this error. In the tutorial, I build ACE and NH2 groups onto the
peptide to neutralize the termini. Since you haven't done this type
of modification, pdb2gmx will die because you have incomplete amides at
the ends of the chain. The "None" terminus instructs pdb2gmx to
not build additional H (in the case of NH2 or NH3+ termini) or O(H) (for
COO- and COOH). It doesn't make any chemical sense to use
"None" for non-capped protein chains.


I don't grasp what specifically Justin meant to say. Could anyone 
one
please help me ? How should I naturalized the termini ?

best regards

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
Department of Mechanical Engineering
Sharif University of Technology, Tehran, Iran


�


�

You can also use g_membed (a GROMACS tool) for the protein insertion. In
the latest GROMACS versions g_membed is part of the mdrun tool (-membed
flag). The reference is Wolf_2010_JC


g_membed is easily combined with LAMBADA as well.

On 19 February 2016 at 10:15, Catarina A. Carvalheda dos Santos <
c.a.c.dossantos
at dundee.ac.uk> wrote:

> Hi Ali,
>
> First create the topology for the protein alone using pdb2gmx.
>
> Then, and if you already have a pre-equilibrated membrane
patch, perform
> the protein alignment and insertion into the membrane. There
are several
> ways to do this (see below).
>
> Align the protein with the membrane:
> - manual procedure/visual inspection (not recommended)
> - based on OPM database information
> - automatic tools: CHARMM-GUI, CELLMICROCOSMOS or LAMBADA
>
> Insert the protein into the membrane:
> - Alchembed Jefferys_2015_JCTC
> 
> - CHARMM-GUI
> - CELLMICROCOSMOS
> - INFLATEGRO2Schmidt_2012_JCIM
> 
>
> I recommend the LAMBADA/INFLATEGRO2 combination.
>
> Keep in mind that automatic tools might fail, so you should
always check
> the output files at each step.
>
> After this, add the lipids to the topology file (number of
lipid molecules
> and lipid parameters) and proceed to solvation, adding ions,
minimization,
> equilibration and then production phase.
>
> I'm not sure if this answers to your question, but I hope
it helps anyway.
>
> Cheers,
>
> On 19 February 2016 at 08:33,  wrote:
>
>>
>>
>>
>> Dear All
>> During researching Internet, I found justin and
Anirban's tutorial
>> about embedding protein
>> in lipid membrane. It was useful and I appreciate them but
I had one
>> question. as I understood, I should make some changes to
protein pdb file
>> ( 1r2h for Ex)
>>  before using it in  pdb2gmx command or the GROMACS
can't
>> keep on and will be died with a fatal error ( something
like adding cope
>> to the ends of the protein ). could
>> somebody please tell me what should I do ? by the way I
found out that
>> Justin's
>> tutorial do something with xleap amber on the pdb file.
>> Please tell me how specifically I should revise my protein
pdb file.
>>
>> best regards
>> Ali khourshaei shargh (khourshaeishargh
at mech.sharif.ir)
>> Department of Mechanical Engineering
>> Sharif University of Technology, Tehran, Iran
>>
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or
>> send a mail to gmx-users-request
at gromacs.org.
>>
>> The University of Dundee is a registered Scottish Charity,

[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Justin


first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
fault not me. also different copies of Email was because of the fact that
I didnt know how to use gmx-user. from now on, I try not to bother my
friends in gmx-user anymore.


to be honest, I need to simulate a cell membrane with 1r2c protein and
exert some tests like creep and compliance onto it to obtain viscoelastic
response of it. after finishing your tutorial, I thought that now I can
do it. I downloaded 1r2c pretin from PDB bank. but unfortunately at the
beginning I confront with fatal error. I really appreciate it if you
answer my below question.


1. the PDB which we usually download from PDB bank is Full length not a
peptide.isnt it?


2. Can I use the full length PDB file or I should change it to obtain a
peptide?


3. about the desired output I explained above, Can I obtain it based on
the method you used in tutorial?


4. If I use gmx pdb2gmx -f 1rc2.pdb -o 1rc2_processed.gro -ignh�
-water spc, I mean without -ter, It says:


Fatal error:

There were 35 missing atoms in molecule Protein_chain_B, if you want to
use this incomplete topology anyhow, use the option -missing


can I keep on using -missing or not?


Finally, I should again thank you because of your helps.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

The tutorial uses a modeled peptide fragment.  Typically fragments of larger
proteins are capped with neutral groups to avoid artifacts of charged termini
that normally wouldnt be there, or to match some experimental data that used
the same form (as is actually the case here).

Dont choose "None" for termini unless you have constructed such
groups.  It
makes no physical or biological sense.  If you have a full-length protein,
these
will have normal termini.  Refer to any basic biochemistry text if you are
unfamiliar with what peptide bonds or protein termini are.

-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




�

�

-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Embedding Protein into lipid bilayer

[khourshaeishargh]

Dear Justin


Thanks for your reply. I think, I got what you mean. By the way, My
protein needs to use BGL residue and of course this type of the residue
isnt available in the gromacs sources. So I find its information in ATP
site and it is attached to my Email as a .itp file. I try to attach its
content to .rtp file  and add BGL to residuetype as protein to
gromos96 53a6, but again when I try to use pdb2gmx command, it fails and
says Residue BGL not found in residue topology database. also the
contents of the attached file isnt as same as the .rtp file writing. Any
Comment ? I really appreciate it.


best regards


Ali


==


Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)


Department of Mechanical Engineering


Sharif University of Technology, Tehran, Iran

Absolutely not.  This will build an incomplete model that is physically
unrealistic.  As a general rule, NEVER use -missing.  It is for niche cases
only.  Check your input PDB structure for obvious MISSING entries that
tell you
about parts of the structure that were not resolved.  If these are internal
residues, you need to build them using the appropriate modeling software (not
GROMACS).

-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


-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Embedding protein into lipid bilayer

[yoochan]

Dear GMX users,

I’m tyring to build lipid and transmembrane(protein) system using 
inflategro.pl. in GROMACS 5.0.4.

I think the inflategro.pl can not build a result on center of box when the 
membrane or lipid are quite large.

Here is my workflow

1. Prepare a protein (1R3J)

2. Prepare a optimized DPPC lipid  (dppc128.gro)

3. Make a large DPPC lipid  using editconf command , because 1R3J is bigger 
than dppc128.gro. (click to show pic 
)

4. Superimpose a protein and newly prepared DPPC lipids (about 1152 dppc 
molecules)

5. Run inflategro.pl as below

$ perl inflategro_1.pl prot_memb.nowater.gro 4 DPPC 5 inflated.gro 5 area.dat

6. Check inflated.gro  (click to show pic) 



Any advices?

Many Thanks,

Yoochan
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding Protein into lipid bilayer

[Catarina A. Carvalheda dos Santos]

Hi Ali,

First create the topology for the protein alone using pdb2gmx.

Then, and if you already have a pre-equilibrated membrane patch, perform
the protein alignment and insertion into the membrane. There are several
ways to do this (see below).

Align the protein with the membrane:
- manual procedure/visual inspection (not recommended)
- based on OPM database information
- automatic tools: CHARMM-GUI, CELLMICROCOSMOS or LAMBADA

Insert the protein into the membrane:
- Alchembed Jefferys_2015_JCTC

- CHARMM-GUI
- CELLMICROCOSMOS
- INFLATEGRO2Schmidt_2012_JCIM


I recommend the LAMBADA/INFLATEGRO2 combination.

Keep in mind that automatic tools might fail, so you should always check
the output files at each step.

After this, add the lipids to the topology file (number of lipid molecules
and lipid parameters) and proceed to solvation, adding ions, minimization,
equilibration and then production phase.

I'm not sure if this answers to your question, but I hope it helps anyway.

Cheers,

On 19 February 2016 at 08:33,  wrote:

>
>
>
> Dear All
> During researching Internet, I found justin and Anirban's tutorial
> about embedding protein
> in lipid membrane. It was useful and I appreciate them but I had one
> question. as I understood, I should make some changes to protein pdb file
> ( 1r2h for Ex)
>  before using it in  pdb2gmx command or the GROMACS can't
> keep on and will be died with a fatal error ( something like adding cope
> to the ends of the protein ). could
> somebody please tell me what should I do ? by the way I found out that
> Justin's
> tutorial do something with xleap amber on the pdb file.
> Please tell me how specifically I should revise my protein pdb file.
>
> best regards
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
> Department of Mechanical Engineering
> Sharif University of Technology, Tehran, Iran
>
> --
> 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 http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding Protein into lipid bilayer

[Catarina A. Carvalheda dos Santos]

You can also use g_membed (a GROMACS tool) for the protein insertion. In
the latest GROMACS versions g_membed is part of the mdrun tool (-membed
flag). The reference is Wolf_2010_JC


g_membed is easily combined with LAMBADA as well.

On 19 February 2016 at 10:15, Catarina A. Carvalheda dos Santos <
c.a.c.dossan...@dundee.ac.uk> wrote:

> Hi Ali,
>
> First create the topology for the protein alone using pdb2gmx.
>
> Then, and if you already have a pre-equilibrated membrane patch, perform
> the protein alignment and insertion into the membrane. There are several
> ways to do this (see below).
>
> Align the protein with the membrane:
> - manual procedure/visual inspection (not recommended)
> - based on OPM database information
> - automatic tools: CHARMM-GUI, CELLMICROCOSMOS or LAMBADA
>
> Insert the protein into the membrane:
> - Alchembed Jefferys_2015_JCTC
> 
> - CHARMM-GUI
> - CELLMICROCOSMOS
> - INFLATEGRO2Schmidt_2012_JCIM
> 
>
> I recommend the LAMBADA/INFLATEGRO2 combination.
>
> Keep in mind that automatic tools might fail, so you should always check
> the output files at each step.
>
> After this, add the lipids to the topology file (number of lipid molecules
> and lipid parameters) and proceed to solvation, adding ions, minimization,
> equilibration and then production phase.
>
> I'm not sure if this answers to your question, but I hope it helps anyway.
>
> Cheers,
>
> On 19 February 2016 at 08:33,  wrote:
>
>>
>>
>>
>> Dear All
>> During researching Internet, I found justin and Anirban's tutorial
>> about embedding protein
>> in lipid membrane. It was useful and I appreciate them but I had one
>> question. as I understood, I should make some changes to protein pdb file
>> ( 1r2h for Ex)
>>  before using it in  pdb2gmx command or the GROMACS can't
>> keep on and will be died with a fatal error ( something like adding cope
>> to the ends of the protein ). could
>> somebody please tell me what should I do ? by the way I found out that
>> Justin's
>> tutorial do something with xleap amber on the pdb file.
>> Please tell me how specifically I should revise my protein pdb file.
>>
>> best regards
>> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
>> Department of Mechanical Engineering
>> Sharif University of Technology, Tehran, Iran
>>
>> --
>> 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 http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
>



-- 
Catarina A. Carvalheda

PhD Student
Computational Biology Division
SLS & SSE
University of Dundee
DD1 5EH, Dundee, Scotland, UK
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding Protein into lipid bilayer

[Justin Lemkul]

Please don't spam the list with many copies of the same message.  People give of 
their free time to answer questions on the list, so it may take a while for 
someone to respond.  Please also make sure your emails are legible; yours are 
littered with bizarre characters.


On 2/20/16 5:30 AM, khourshaeisha...@mech.sharif.ir wrote:




pre.cjk { font-family: "Nimbus Mono L",monospace; }p { margin-bottom:
0.1in; line-height: 120%; }a:link {  }


Hi Catarina


Thanks for your reply, I really appreciate it. you know, I complete
Justin's Tutorial, so I know what procedures I should do. but now I
want to embed 2rh1 protein into DPPC lipid bilayer� which I already
downloaded it from rcsb.com.� when I tried to use pdb2gmx� via
"gmx pdb2gmx -f 2rh1.pdb -o 2rh1_processed.gro -ignh -ter -water
spc", it says :




�


Select start terminus type for ASP-29

�0: NH3+

�1: NH2

�2: None

2

Start terminus ASP-29: None

Select end terminus type for LEU-342

�0: COO-

�1: COOH

�2: None

2

End terminus LEU-342: None

---

Program gmx, VERSION 5.0.5

Source code file:
/home/ali/gromacs-5.0.5/src/gromacs/gmxpreprocess/pdb2top.cpp, line:
1091



Fatal error:

There is a dangling bond at at least one of the terminal ends. Fix your
coordinate file, add a new terminal database entry (.tdb), or select the
proper existing terminal entry.

---


I found a similar question in which Justin replied it as below :


You haven't added caps onto the input protein, you should expect to
get this error. In the tutorial, I build ACE and NH2 groups onto the
peptide to neutralize the termini. Since you haven't done this type
of modification, pdb2gmx will die because you have incomplete amides at
the ends of the chain. The "None" terminus instructs pdb2gmx to
not build additional H (in the case of NH2 or NH3+ termini) or O(H) (for
COO- and COOH). It doesn't make any chemical sense to use
"None" for non-capped protein chains.


I don't grasp what specifically Justin meant to say. Could anyone 
one
please help me ? How should I naturalized the termini ?



The tutorial uses a modeled peptide fragment.  Typically fragments of larger 
proteins are capped with neutral groups to avoid artifacts of charged termini 
that normally wouldn't be there, or to match some experimental data that used 
the same form (as is actually the case here).


Don't choose "None" for termini unless you have constructed such groups.  It 
makes no physical or biological sense.  If you have a full-length protein, these 
will have normal termini.  Refer to any basic biochemistry text if you are 
unfamiliar with what peptide bonds or protein termini are.


-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

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding Protein into lipid bilayer

[Justin Lemkul]

On 2/21/16 5:44 AM, khourshaeisha...@mech.sharif.ir wrote:




p { margin-bottom: 0.1in; line-height: 120%; }a:link {  }


Dear Justin


first of all, thanks for your replay. but I should cite that the bizarre
character that you saw in my Email was Sharif university Email domains
fault not me. also different copies of Email was because of the fact that
I didnt know how to use gmx-user. from now on, I try not to bother my
friends in gmx-user anymore.


to be honest, I need to simulate a cell membrane with 1r2c protein and
exert some tests like creep and compliance onto it to obtain viscoelastic
response of it. after finishing your tutorial, I thought that now I can
do it. I downloaded 1r2c pretin from PDB bank. but unfortunately at the
beginning I confront with fatal error. I really appreciate it if you
answer my below question.


1. the PDB which we usually download from PDB bank is Full length not a
peptide.isnt it?



Depends on the protein.



2. Can I use the full length PDB file or I should change it to obtain a
peptide?



Simulate whatever is relevant to your scientific question(s) at hand.  You do 
not need to conform to some simple tutorial example.  Tutorials are, by design, 
some small and reproducible system.  "Real" science is often much more complex.




3. about the desired output I explained above, Can I obtain it based on
the method you used in tutorial?



I don't really know what any of that is.  Use literature as your guide.  The 
tutorial is a simple how-to for setting up a heterogeneous system.  How you 
carry out and analyze the subsequent simulation depends entirely upon what you 
want to observe.




4. If I use gmx pdb2gmx -f 1rc2.pdb -o 1rc2_processed.gro -ignh�
-water spc, I mean without -ter, It says:


Fatal error:

There were 35 missing atoms in molecule Protein_chain_B, if you want to
use this incomplete topology anyhow, use the option -missing


can I keep on using -missing or not?



Absolutely not.  This will build an incomplete model that is physically 
unrealistic.  As a general rule, NEVER use -missing.  It is for niche cases 
only.  Check your input PDB structure for obvious MISSING entries that tell you 
about parts of the structure that were not resolved.  If these are internal 
residues, you need to build them using the appropriate modeling software (not 
GROMACS).


-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

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding Protein into lipid bilayer

[Justin Lemkul]

On 2/22/16 4:40 AM, khourshaeisha...@mech.sharif.ir wrote:





Dear Justin


Thanks for your reply. I think, I got what you mean. By the way, My
protein needs to use BGL residue and of course this type of the residue
isnt available in the gromacs sources. So I find its information in ATP
site and it is attached to my Email as a .itp file. I try to attach its


The mailing list does not accept attachments.


content to .rtp file  and add BGL to residuetype as protein to
gromos96 53a6, but again when I try to use pdb2gmx command, it fails and
says Residue BGL not found in residue topology database. also the
contents of the attached file isnt as same as the .rtp file writing. Any
Comment ? I really appreciate it.



Follow 
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field


-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

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding protein into lipid bilayer

[Justin Lemkul]

On 3/6/15 11:02 PM, yoochan wrote:

Dear GMX users,

I’m tyring to build lipid and transmembrane(protein) system using 
inflategro.pl. in GROMACS 5.0.4.

I think the inflategro.pl can not build a result on center of box when the 
membrane or lipid are quite large.



That's not likely true.


Here is my workflow

1. Prepare a protein (1R3J)

2. Prepare a optimized DPPC lipid  (dppc128.gro)

3. Make a large DPPC lipid  using editconf command , because 1R3J is bigger than 
dppc128.gro. (click to show pic 
)

4. Superimpose a protein and newly prepared DPPC lipids (about 1152 dppc 
molecules)

5. Run inflategro.pl as below

$ perl inflategro_1.pl prot_memb.nowater.gro 4 DPPC 5 inflated.gro 5 area.dat

6. Check inflated.gro  (click to show pic) 




This image suggests that you haven't prepared the system correctly (either step 
3 or 4, or both).  If the protein is off-center from the lipids, that comes from 
incorrect initial placement.


-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

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Embedding protein into lipid bilayer

[yoochan]

Justin Lemkul  writes:

> 
> 
> On 3/6/15 11:02 PM, yoochan wrote:
> > Dear GMX users,
> >
> > I’m tyring to build lipid and transmembrane(protein) system using 
> > inflategro.pl. in GROMACS 5.0.4.
> >
> > I think the inflategro.pl can not build a result on center of box when the 
> > membrane or lipid are quite large.
> >
> 
> That's not likely true.
> 
> > Here is my workflow
> >
> > 1. Prepare a protein (1R3J)
> >
> > 2. Prepare a optimized DPPC lipid  (dppc128.gro)
> >
> > 3. Make a large DPPC lipid  using editconf command , because 1R3J is bigger 
> > than dppc128.gro. (click to show
> pic 
> )
> >
> > 4. Superimpose a protein and newly prepared DPPC lipids (about 1152 dppc 
> > molecules)
> >
> > 5. Run inflategro.pl as below
> >
> > $ perl inflategro_1.pl prot_memb.nowater.gro 4 DPPC 5 inflated.gro 5 
> > area.dat
> >
> > 6. Check inflated.gro  (click to show pic) 
> > 
> >
> 
> This image suggests that you haven't prepared the system correctly (either 
> step 
> 3 or 4, or both).  If the protein is off-center from the lipids, that comes 
> from 
> incorrect initial placement.
> 
> -Justin
> 

Thank you for your message.

The picture of preparation process looks weird but I think preparation has done 
correctly.

The transmembrane region of protein is well located on center of DPPC bilayer.
 
Here, I attach different angle of views about previous picture.

(Top View : https://www.dropbox.com/s/omn1haq3u2psp6v/top.png?dl=0)
(Side View : https://www.dropbox.com/s/9kg05gxi1m0312m/side.png?dl=0)

There is no problem when I run Inflategro.pl with small amounts of DPPC bilayer.

I have no idea about this issue.

Many Thanks,

Yoochan
-- 
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 http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.