Re: [gmx-users] POPC in water

[Justin A. Lemkul]

On 7/10/12 6:09 AM, Shima Arasteh wrote:

Dear gmx users,


I want to simulate a protein in bilayer. The chosen bilayer is POPC.
According to Justin's tutorial about KALP15 in DPPC, I would simulate the
protein in lipid bilayer and water. In this tutorial I didn't find the
simulation of bilayer in water seperately and it is just going through the
simulation with protein.



See part 1 of step 3:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

It's not a full simulation of a membrane, but it presents all the essential 
elements - coordinate file, topology (very simple), and .mdp (though it is for 
EM, not an MD simulation).



I need to say that I got the POPC.itp and .top through the link sent me by
dear Peter.


Now I'm wondering if POPC is needed to simulate in water before applying in
simulation of protein in POPC?



The answer depends on how well equilibrated the starting structure is.  If 
you're going to be putting a protein in it, you'll have to re-equilibrate that 
new system for a considerable amount of time, so simulating the membrane 
beforehand may or may not be relevant, but a thoroughly equilibrated membrane 
will reduce the time needed in equilibrating the membrane protein system.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




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Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

[Anirban Ghosh]

Thanks Angel and Justin.
Will try out the options!

Regards,

-Anirban

On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul  wrote:

>
>
> On 5/1/12 8:05 AM, Ángel Piñeiro wrote:
>
>> I guess there are better solutions but an alternative is to map your
>> bilayer to
>> MARTINI 
>> (http://md.chem.rug.nl/**cgmartini/)
>> and then to use SUGAR-PIE
>> (http://smmb.usc.es/sugarpie/**sugarpie.php)
>> to go to from MARTINI to all-atom
>> CHARMM36.
>>
>>
> Even simpler would be to fix the offending atom names and build a suitable
> .hdb entry (if one does not already exist) and produce the topology with
> pdb2gmx.  I would think it would then be far easier to preserve the
> original configurations of the lipids, rather than changing the resolution
> back and forth.
>
> -Justin
>
>  Hope it helps,
>>
>> Ángel.
>>
>>
>> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:
>>
>>> Hi ALL,
>>>
>>>
>>> I have a equilibrated POPC bilayer (100 ns run) that I have run using
>>> GROMOS
>>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
>>> using
>>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
>>> conventions
>>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives
>>> error.
>>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC
>>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot
>>> in
>>> advance.
>>>
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Anirban
>>> --
>>> gmx-users mailing listgmx-us...@gromacs.org  >> gmx-users@gromacs.org>
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>>
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

[Justin A. Lemkul]

On 5/1/12 8:05 AM, Ángel Piñeiro wrote:

I guess there are better solutions but an alternative is to map your bilayer to
MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE
(http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom
CHARMM36.



Even simpler would be to fix the offending atom names and build a suitable .hdb 
entry (if one does not already exist) and produce the topology with pdb2gmx.  I 
would think it would then be far easier to preserve the original configurations 
of the lipids, rather than changing the resolution back and forth.


-Justin


Hope it helps,

Ángel.


On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:

Hi ALL,


I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS
ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using
CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions
(N, P, C, O) between this two FFs as a result of which pdb2gmx gives error.
Can these atom names (hydrogens can be ignored) of my equilibrated POPC
bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in
advance.




Regards,


Anirban
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

[Ángel Piñeiro]

I guess there are better solutions but an alternative is to map your
bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use
SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from
MARTINI to all-atom CHARMM36.

Hope it helps,

Ángel.


On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:

> Hi ALL,
> 
> 
> 
> I have a equilibrated POPC bilayer (100 ns run) that I have run using
> GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new
> simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences
> in atom naming conventions (N, P, C, O) between this two FFs as a
> result of which pdb2gmx gives error. Can these atom names (hydrogens
> can be ignored) of my equilibrated POPC bilayer be changed manually
> and then used with CHARMM36 FF? Thanks a lot in advance.
> 
> 
> 
> 
> Regards,
> 
> 
> Anirban
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
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RE: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Kukol, Andreas]

I am not sure about your workaround, how to shift something.
The updated topology contains the correct potential phi2 as described in the 
publication, but it is expressed with Ryckaert-Bellemans potentials.

Andreas

---

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Alex Smolyanitsky
Sent: 03 May 2010 21:32
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Thanks Andreas.

Is there any difference force-wise between this and our little workaround?

Alex


On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas  wrote:
Hi,

The POPC_53a6 topology works only with Gromacs versions lower than 4. Please 
find attached the topology compatible with Gromacs4.

I shall update files on the Gromacs website. Sorry for causing confusion.

Best wishes
Andreas


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Alex Smolyanitsky [asmol...@asu.edu]
Sent: 03 May 2010 18:22
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are 
concerned, these dihedrals can be commented out. When considering the energy 
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole 
mailto:x.peri...@rug.nl>> wrote:

HAve look at the paper describing the topology ...


On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:

Hello everyone,

I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( 
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
 ) for a simple lipid in water sim (gromacs version 4.0.5).

I am using the lipid coordinates from the same archive and here's my topology:
***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0, 
which is smaller than the minimum of 1" without any prior warnings.
The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these dihedrals have 
zero equilibrium angle and a multiplicity of 3:

...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these dihedrals by 
setting a multiplicity of zero? Or, should these two be set according to the 
older topology? I know similar questions have been asked here in the past, but 
I really want to make sure my topology is sane. Thanks a lot.

Alex
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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Thanks Andreas.

Is there any difference force-wise between this and our little workaround?

Alex


On Mon, May 3, 2010 at 2:17 PM, Kukol, Andreas  wrote:

> Hi,
>
> The POPC_53a6 topology works only with Gromacs versions lower than 4.
> Please find attached the topology compatible with Gromacs4.
>
> I shall update files on the Gromacs website. Sorry for causing confusion.
>
> Best wishes
> Andreas
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On
> Behalf Of Alex Smolyanitsky [asmol...@asu.edu]
> Sent: 03 May 2010 18:22
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)
>
> Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.
>
> Just in case anyone else is faced with the same issue, as far as forces are
> concerned, these dihedrals can be commented out. When considering the energy
> associated with dihedrals, just shift it appropriately.
> On Mon, May 3, 2010 at 10:57 AM, XAvier Periole  x.peri...@rug.nl>> wrote:
>
> HAve look at the paper describing the topology ...
>
>
> On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:
>
> Hello everyone,
>
> I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
>  for a simple lipid in water sim (gromacs version 4.0.5).
>
> I am using the lipid coordinates from the same archive and here's my
> topology:
> ***
> #include "ffG53a6.itp"
> #include "popc_53a6.itp"
> #include "spc.itp"
>
> [ system ]
> ;Name
> test
>
> [ molecules ]
> POPC  128
> SOL   3585
> ***
>
> grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
> which is smaller than the minimum of 1" without any prior warnings.
> The error has to do with two dihedral angles with zero multiplicity:
>
> ...
> 22   23   24   25   1   90   -5.685   0
> ...
> 24   25   26   27   1   90   -5.685   0
> ...
>
> So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
> have zero equilibrium angle and a multiplicity of 3:
>
> ...
> 22   23   24   25   1   0.0   5.858   3
> ...
> 24   25   26   27   1   0.0   5.858   3
> ...
>
> Did the author of the 53a6 topology want to simply remove these dihedrals
> by setting a multiplicity of zero? Or, should these two be set according to
> the older topology? I know similar questions have been asked here in the
> past, but I really want to make sure my topology is sane. Thanks a lot.
>
> Alex
> --
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RE: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Kukol, Andreas]

Hi,

The POPC_53a6 topology works only with Gromacs versions lower than 4. Please 
find attached the topology compatible with Gromacs4.

I shall update files on the Gromacs website. Sorry for causing confusion.

Best wishes
Andreas


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of Alex Smolyanitsky [asmol...@asu.edu]
Sent: 03 May 2010 18:22
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are 
concerned, these dihedrals can be commented out. When considering the energy 
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole 
mailto:x.peri...@rug.nl>> wrote:

HAve look at the paper describing the topology ...


On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:

Hello everyone,

I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip ( 
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies
 ) for a simple lipid in water sim (gromacs version 4.0.5).

I am using the lipid coordinates from the same archive and here's my topology:
***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0, 
which is smaller than the minimum of 1" without any prior warnings.
The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these dihedrals have 
zero equilibrium angle and a multiplicity of 3:

...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these dihedrals by 
setting a multiplicity of zero? Or, should these two be set according to the 
older topology? I know similar questions have been asked here in the past, but 
I really want to make sure my topology is sane. Thanks a lot.

Alex
--
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popcGromacs4_53a6.itp
Description: popcGromacs4_53a6.itp
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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[Alex Smolyanitsky]

Yup, those are indeed constants associated with phi2 (Fig. 1(B)), thanks.

Just in case anyone else is faced with the same issue, as far as forces are
concerned, these dihedrals can be commented out. When considering the energy
associated with dihedrals, just shift it appropriately.
On Mon, May 3, 2010 at 10:57 AM, XAvier Periole  wrote:

>
> HAve look at the paper describing the topology ...
>
>
>   On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:
>
>   Hello everyone,
>
> I am trying to include a POPC 53a6 topology from LipidsForGro96_53a6.zip (
> http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies)
>  for a simple lipid in water sim (gromacs version 4.0.5).
>
> I am using the lipid coordinates from the same archive and here's my
> topology:
> ***
> #include "ffG53a6.itp"
> #include "popc_53a6.itp"
> #include "spc.itp"
>
> [ system ]
> ;Name
> test
>
> [ molecules ]
> POPC  128
> SOL   3585
> ***
>
> grompp throws a fatal error: " Value of 'multiplicity' in Proper Dih. is 0,
> which is smaller than the minimum of 1" without any prior warnings.
> The error has to do with two dihedral angles with zero multiplicity:
>
> ...
> 22   23   24   25   1   90   -5.685   0
> ...
> 24   25   26   27   1   90   -5.685   0
> ...
>
> So I looked at an ancient POPC topology for GROMOS87 and these dihedrals
> have zero equilibrium angle and a multiplicity of 3:
>
>  ...
> 22   23   24   25   1   0.0   5.858   3
> ...
> 24   25   26   27   1   0.0   5.858   3
> ...
>
> Did the author of the 53a6 topology want to simply remove these dihedrals
> by setting a multiplicity of zero? Or, should these two be set according to
> the older topology? I know similar questions have been asked here in the
> past, but I really want to make sure my topology is sane. Thanks a lot.
>
> Alex
> --
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Re: [gmx-users] POPC 53a6 topology (dihedral multiplicity)

[XAvier Periole]

HAve look at the paper describing the topology ...


On May 3, 2010, at 6:52 PM, Alex Smolyanitsky wrote:


Hello everyone,

I am trying to include a POPC 53a6 topology from  
LipidsForGro96_53a6.zip ( http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies 
 ) for a simple lipid in water sim (gromacs version 4.0.5).


I am using the lipid coordinates from the same archive and here's my  
topology:

***
#include "ffG53a6.itp"
#include "popc_53a6.itp"
#include "spc.itp"

[ system ]
;Name
test

[ molecules ]
POPC  128
SOL   3585
***

grompp throws a fatal error: " Value of 'multiplicity' in Proper  
Dih. is 0, which is smaller than the minimum of 1" without any prior  
warnings.

The error has to do with two dihedral angles with zero multiplicity:

...
22   23   24   25   1   90   -5.685   0
...
24   25   26   27   1   90   -5.685   0
...

So I looked at an ancient POPC topology for GROMOS87 and these  
dihedrals have zero equilibrium angle and a multiplicity of 3:


...
22   23   24   25   1   0.0   5.858   3
...
24   25   26   27   1   0.0   5.858   3
...

Did the author of the 53a6 topology want to simply remove these  
dihedrals by setting a multiplicity of zero? Or, should these two be  
set according to the older topology? I know similar questions have  
been asked here in the past, but I really want to make sure my  
topology is sane. Thanks a lot.


Alex
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Re: [gmx-users] POPC Membrane + protein dynamics

[ravi sharma]

Thanx Justin,

I am somewhat faraway from the topic so can't remember clearly how to define. 
may be you are right. But this the case where i stuck before.



regards,

Ravi Datta Sharma  Lecturer,  Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
  


--- On Sat, 27/3/10, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] POPC Membrane + protein dynamics
To: "Gromacs Users' List" 
Date: Saturday, 27 March, 2010, 4:59 PM



ravi sharma wrote:
> 
> Dear,
> This is the case when you added some ions in your pdb but not define it in 
> your topology, Go in the end of you topology and subtract the number of 
> molecule added. Also define the number of ions added and the name of the ion.
> like :
> NA     14
> 

Addition of ions is one possibility, but is not definitively the answer here, 
especially since the difference in atoms is on the order of 10,000 (roughly 20% 
of the atoms in the system).  In the case of the original post, it is far more 
likely that there is something more fundamentally wrong with the topology.

Addition of molecules to the topology requires the molecule name, not the atom 
name, be added to the [molecules] directive.  I don't know any force field in 
Gromacs that uses "NA" as a molecule name; they are all either Na, Na+, or 
NA+.  Any number of molecules subtracted must come from the group in which they 
are embedded, not just some generic "number of molecules" (stated for the sake 
of clarity).

-Justin

> 
> 
> regards,
> Ravi
> 
>                                                          
> 
> --- On *Sat, 27/3/10, Justin A. Lemkul //* wrote:
> 
> 
>     From: Justin A. Lemkul 
>     Subject: Re: [gmx-users] POPC Membrane + protein dynamics
>     To: "Gromacs Users' List" 
>     Date: Saturday, 27 March, 2010, 1:50 AM
> 
> 
> 
>     pa...@ncbs.res.in  wrote:
>      > hi
>      > i have tried as per your justin lemkul's tutorial.
>      >
>      > after aligning the protein with membrane, subsequently we tried
>     to use
>      > grompp to generate a tpr file i got the following error.
>      >
>      > ---
>      > Program grompp_mpi, VERSION 3.3.1
>      > Source code file: grompp.c, line: 448
>      >
>      > Fatal error:
>      > number of coordinates in coordinate file (pope.pdb, 37867)
>      >              does not match topology (topol_pope.top, 46779)
>      > ---
>      >
>      > can any one have idea about how to solve this error.
>      >
> 
>     Please see the general advice:
> 
>     
>http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> 
>     Beyond that, you'll have to post greater details of what step is
>     giving rise to this error, what you have done as far as inserting
>     the protein, adding solvent and/or ions, etc.
> 
>     I would also recommend using the latest version of Gromacs (4.0.7),
>     unless for some reason you have to use an ancient version (3.3.1).     
>The speed upgrade is incredible :)
> 
>     -Justin
> 
>      > thanks in advance,
>      > Padhu.
>      >
>      >>
>      >> pa...@ncbs.res.in  wrote:
>      >>> Dear All,
>      >>> I'm a new comer to gromacs. I need to perform molecular dynamics
>      >>> simulation of my protein within the POPC membrane. I have
>     downloaded the
>      >>> 128a popc lipid from Prof.Tieleman's group along with the required
>      >>> popc.itp. My protein of interest is 458 residues. Since the
>     128a popc is
>      >>> already Simulated for 1600 ps, i haven't done membrane only
>     simulation.
>      >>> So
>      >>> i directly aligned my protein with the membrane using VMD and
>     have saved
>      >>> the coordinates. However after i aligned my protein with the
>     membrane, i
>      >>> felt the membrane was not big enough for my protein of
>     interest, also,
>      >>> the
>      >>> N-terminal region and the loop regions in the C-terminal region and
>      >>> stretching outside water molecule above and below
>     respectively.ow, i
>      >>> have
>      >>> two questions here...
>      >> Yep, if the protein is sticking "out" of the box on both sides,
>     the box is
>      >> too
>      >> small.
>      >>
>      >&g

Re: [gmx-users] POPC Membrane + protein dynamics

[Justin A. Lemkul]

ravi sharma wrote:


Dear,
This is the case when you added some ions in your pdb but not define it 
in your topology, Go in the end of you topology and subtract the number 
of molecule added. Also define the number of ions added and the name of 
the ion.

like :
NA 14



Addition of ions is one possibility, but is not definitively the answer here, 
especially since the difference in atoms is on the order of 10,000 (roughly 20% 
of the atoms in the system).  In the case of the original post, it is far more 
likely that there is something more fundamentally wrong with the topology.


Addition of molecules to the topology requires the molecule name, not the atom 
name, be added to the [molecules] directive.  I don't know any force field in 
Gromacs that uses "NA" as a molecule name; they are all either Na, Na+, or NA+. 
 Any number of molecules subtracted must come from the group in which they are 
embedded, not just some generic "number of molecules" (stated for the sake of 
clarity).


-Justin




regards,
Ravi

 



--- On *Sat, 27/3/10, Justin A. Lemkul //* wrote:


From: Justin A. Lemkul 
    Subject: Re: [gmx-users] POPC Membrane + protein dynamics
To: "Gromacs Users' List" 
Date: Saturday, 27 March, 2010, 1:50 AM



pa...@ncbs.res.in  wrote:
 > hi
 > i have tried as per your justin lemkul's tutorial.
 >
 > after aligning the protein with membrane, subsequently we tried
to use
 > grompp to generate a tpr file i got the following error.
 >
 > ---
 > Program grompp_mpi, VERSION 3.3.1
 > Source code file: grompp.c, line: 448
 >
 > Fatal error:
 > number of coordinates in coordinate file (pope.pdb, 37867)
 >  does not match topology (topol_pope.top, 46779)
 > ---
 >
 > can any one have idea about how to solve this error.
 >

Please see the general advice:


http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Beyond that, you'll have to post greater details of what step is
giving rise to this error, what you have done as far as inserting
the protein, adding solvent and/or ions, etc.

I would also recommend using the latest version of Gromacs (4.0.7),
unless for some reason you have to use an ancient version (3.3.1). 
The speed upgrade is incredible :)


-Justin

 > thanks in advance,
 > Padhu.
 >
 >>
 >> pa...@ncbs.res.in  wrote:
 >>> Dear All,
 >>> I'm a new comer to gromacs. I need to perform molecular dynamics
 >>> simulation of my protein within the POPC membrane. I have
downloaded the
 >>> 128a popc lipid from Prof.Tieleman's group along with the required
 >>> popc.itp. My protein of interest is 458 residues. Since the
128a popc is
 >>> already Simulated for 1600 ps, i haven't done membrane only
simulation.
 >>> So
 >>> i directly aligned my protein with the membrane using VMD and
have saved
 >>> the coordinates. However after i aligned my protein with the
membrane, i
 >>> felt the membrane was not big enough for my protein of
interest, also,
 >>> the
 >>> N-terminal region and the loop regions in the C-terminal region and
 >>> stretching outside water molecule above and below
respectively.ow, i
 >>> have
 >>> two questions here...
 >> Yep, if the protein is sticking "out" of the box on both sides,
the box is
 >> too
 >> small.
 >>
 >>> 1. How would i increase the number of lipids from the existing one?
 >> Two options:
 >>
 >> 1. genconf -nbox will give integer multiples of the lipid system
(i.e.,
 >> -nbox 2
 >> 2 1 will expand the bilayer in the x and y directions and give
512 lipids)
 >>
 >> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you
a bit
 >> finer
 >> control over how large the box is and how many lipids will result.
 >>
 >>> 2. Also, i should increase increase the number of water
molecules above
 >>> and below the membrane so that it covers the whole region of
N-terminal
 >>> and also the loop regions of the C-terminal.
 >> Expand the box using editconf and add solvent with genbox.
 >>
 >>> Now, How to perform these tasks??If i do so will it be
compatible with
 >>> the

Re: [gmx-users] POPC Membrane + protein dynamics

[ravi sharma]

Dear,
This is the case when you added some ions in your pdb but not define it in your 
topology, Go in the end of you topology and subtract the number of molecule 
added. Also define the number of ions added and the name of the ion.
like :
NA 14



regards,
Ravi

  


--- On Sat, 27/3/10, Justin A. Lemkul  wrote:

From: Justin A. Lemkul 
Subject: Re: [gmx-users] POPC Membrane + protein dynamics
To: "Gromacs Users' List" 
Date: Saturday, 27 March, 2010, 1:50 AM



pa...@ncbs.res.in wrote:
> hi
> i have tried as per your justin lemkul's tutorial.
> 
> after aligning the protein with membrane, subsequently we tried to use
> grompp to generate a tpr file i got the following error.
> 
> ---
> Program grompp_mpi, VERSION 3.3.1
> Source code file: grompp.c, line: 448
> 
> Fatal error:
> number of coordinates in coordinate file (pope.pdb, 37867)
>              does not match topology (topol_pope.top, 46779)
> ---
> 
> can any one have idea about how to solve this error.
> 

Please see the general advice:

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Beyond that, you'll have to post greater details of what step is giving rise to 
this error, what you have done as far as inserting the protein, adding solvent 
and/or ions, etc.

I would also recommend using the latest version of Gromacs (4.0.7), unless for 
some reason you have to use an ancient version (3.3.1).  The speed upgrade is 
incredible :)

-Justin

> thanks in advance,
> Padhu.
> 
>> 
>> pa...@ncbs.res.in wrote:
>>> Dear All,
>>> I'm a new comer to gromacs. I need to perform molecular dynamics
>>> simulation of my protein within the POPC membrane. I have downloaded the
>>> 128a popc lipid from Prof.Tieleman's group along with the required
>>> popc.itp. My protein of interest is 458 residues. Since the 128a popc is
>>> already Simulated for 1600 ps, i haven't done membrane only simulation.
>>> So
>>> i directly aligned my protein with the membrane using VMD and have saved
>>> the coordinates. However after i aligned my protein with the membrane, i
>>> felt the membrane was not big enough for my protein of interest, also,
>>> the
>>> N-terminal region and the loop regions in the C-terminal region and
>>> stretching outside water molecule above and below respectively.ow, i
>>> have
>>> two questions here...
>> Yep, if the protein is sticking "out" of the box on both sides, the box is
>> too
>> small.
>> 
>>> 1. How would i increase the number of lipids from the existing one?
>> Two options:
>> 
>> 1. genconf -nbox will give integer multiples of the lipid system (i.e.,
>> -nbox 2
>> 2 1 will expand the bilayer in the x and y directions and give 512 lipids)
>> 
>> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit
>> finer
>> control over how large the box is and how many lipids will result.
>> 
>>> 2. Also, i should increase increase the number of water molecules above
>>> and below the membrane so that it covers the whole region of N-terminal
>>> and also the loop regions of the C-terminal.
>> Expand the box using editconf and add solvent with genbox.
>> 
>>> Now, How to perform these tasks??If i do so will it be compatible with
>>> the
>>> p
> 
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] POPC Membrane + protein dynamics

[Justin A. Lemkul]

pa...@ncbs.res.in wrote:

hi
i have tried as per your justin lemkul's tutorial.

after aligning the protein with membrane, subsequently we tried to use
grompp to generate a tpr file i got the following error.

---
Program grompp_mpi, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (pope.pdb, 37867)
 does not match topology (topol_pope.top, 46779)
---

can any one have idea about how to solve this error.



Please see the general advice:

http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology

Beyond that, you'll have to post greater details of what step is giving rise to 
this error, what you have done as far as inserting the protein, adding solvent 
and/or ions, etc.


I would also recommend using the latest version of Gromacs (4.0.7), unless for 
some reason you have to use an ancient version (3.3.1).  The speed upgrade is 
incredible :)


-Justin


thanks in advance,
Padhu.



pa...@ncbs.res.in wrote:

Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
simulation of my protein within the POPC membrane. I have downloaded the
128a popc lipid from Prof.Tieleman's group along with the required
popc.itp. My protein of interest is 458 residues. Since the 128a popc is
already Simulated for 1600 ps, i haven't done membrane only simulation.
So
i directly aligned my protein with the membrane using VMD and have saved
the coordinates. However after i aligned my protein with the membrane, i
felt the membrane was not big enough for my protein of interest, also,
the
N-terminal region and the loop regions in the C-terminal region and
stretching outside water molecule above and below respectively.ow, i
have
two questions here...

Yep, if the protein is sticking "out" of the box on both sides, the box is
too
small.


1. How would i increase the number of lipids from the existing one?

Two options:

1. genconf -nbox will give integer multiples of the lipid system (i.e.,
-nbox 2
2 1 will expand the bilayer in the x and y directions and give 512 lipids)

2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit
finer
control over how large the box is and how many lipids will result.


2. Also, i should increase increase the number of water molecules above
and below the membrane so that it covers the whole region of N-terminal
and also the loop regions of the C-terminal.

Expand the box using editconf and add solvent with genbox.


Now, How to perform these tasks??If i do so will it be compatible with
the
p





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] POPC Membrane + protein dynamics

[padhu]

hi
i have tried as per your justin lemkul's tutorial.

after aligning the protein with membrane, subsequently we tried to use
grompp to generate a tpr file i got the following error.

---
Program grompp_mpi, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (pope.pdb, 37867)
 does not match topology (topol_pope.top, 46779)
---

can any one have idea about how to solve this error.

thanks in advance,
Padhu.

>
>
> pa...@ncbs.res.in wrote:
>> Dear All,
>> I'm a new comer to gromacs. I need to perform molecular dynamics
>> simulation of my protein within the POPC membrane. I have downloaded the
>> 128a popc lipid from Prof.Tieleman's group along with the required
>> popc.itp. My protein of interest is 458 residues. Since the 128a popc is
>> already Simulated for 1600 ps, i haven't done membrane only simulation.
>> So
>> i directly aligned my protein with the membrane using VMD and have saved
>> the coordinates. However after i aligned my protein with the membrane, i
>> felt the membrane was not big enough for my protein of interest, also,
>> the
>> N-terminal region and the loop regions in the C-terminal region and
>> stretching outside water molecule above and below respectively.ow, i
>> have
>> two questions here...
>
> Yep, if the protein is sticking "out" of the box on both sides, the box is
> too
> small.
>
>> 1. How would i increase the number of lipids from the existing one?
>
> Two options:
>
> 1. genconf -nbox will give integer multiples of the lipid system (i.e.,
> -nbox 2
> 2 1 will expand the bilayer in the x and y directions and give 512 lipids)
>
> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit
> finer
> control over how large the box is and how many lipids will result.
>
>> 2. Also, i should increase increase the number of water molecules above
>> and below the membrane so that it covers the whole region of N-terminal
>> and also the loop regions of the C-terminal.
>
> Expand the box using editconf and add solvent with genbox.
>
>> Now, How to perform these tasks??If i do so will it be compatible with
>> the
>> p

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Re: [gmx-users] POPC Membrane + protein dynamics

[padhu]

Dear Justin,
Many thanks for your comprehensive mail. I will try to do it and let you
know if i come across any problem..(Definetely i may bug u again :))
Thank you so much.
Best regards
Padhu

>
>
> pa...@ncbs.res.in wrote:
>> Dear All,
>> I'm a new comer to gromacs. I need to perform molecular dynamics
>> simulation of my protein within the POPC membrane. I have downloaded the
>> 128a popc lipid from Prof.Tieleman's group along with the required
>> popc.itp. My protein of interest is 458 residues. Since the 128a popc is
>> already Simulated for 1600 ps, i haven't done membrane only simulation.
>> So
>> i directly aligned my protein with the membrane using VMD and have saved
>> the coordinates. However after i aligned my protein with the membrane, i
>> felt the membrane was not big enough for my protein of interest, also,
>> the
>> N-terminal region and the loop regions in the C-terminal region and
>> stretching outside water molecule above and below respectively.ow, i
>> have
>> two questions here...
>
> Yep, if the protein is sticking "out" of the box on both sides, the box is
> too
> small.
>
>> 1. How would i increase the number of lipids from the existing one?
>
> Two options:
>
> 1. genconf -nbox will give integer multiples of the lipid system (i.e.,
> -nbox 2
> 2 1 will expand the bilayer in the x and y directions and give 512 lipids)
>
> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit
> finer
> control over how large the box is and how many lipids will result.
>
>> 2. Also, i should increase increase the number of water molecules above
>> and below the membrane so that it covers the whole region of N-terminal
>> and also the loop regions of the C-terminal.
>
> Expand the box using editconf and add solvent with genbox.
>
>> Now, How to perform these tasks??If i do so will it be compatible with
>> the
>> popc.itp file which i downloaded from the Prof. Tieleman's group?
>>
>
> None of the above operations have any influence on the parameters
> contained in
> popc.itp.  If you are unsure about Gromacs workflows, file formats, etc.
> then
> you really need read the manual and do some more basic tutorial material
> before
> you attempt a difficult simulation like a membrane protein.  There are a
> lot of
> pitfalls in simulating such a complex system, and if you are not ready for
> them,
> then you can waste a whole lot of time generating nonsensical results :)
>
>> 3. My third question is while aligning my protein with the membrane
>> should
>> i make a hole first or after aligning the protein should i remove the
>> overlapping lipids with the proteins?which one would be better??
>>
>
> There are several methods for doing this.  See below.
>
>> I have tried out some of the methodologies available in the internet but
>> it dosen't help me.If anyone of you have a detailed step by step
>> methodology right from the first step to till running the MD simulation
>> please let me know.
>
> Saying you've tried things and they didn't work is useless.  What did you
> try?
> What links can you provide?  Have you tried the membrane protein tutorial
> linked
> from the Gromacs site?  That's about as step-by-step as it gets.
>
> -Justin
>
>> Your help will be highly appreciated.
>> Looking forward to hear from you.
>>
>> Best regards
>> Padmanabhan
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] POPC Membrane + protein dynamics

[Justin A. Lemkul]

pa...@ncbs.res.in wrote:

Dear All,
I'm a new comer to gromacs. I need to perform molecular dynamics
simulation of my protein within the POPC membrane. I have downloaded the
128a popc lipid from Prof.Tieleman's group along with the required
popc.itp. My protein of interest is 458 residues. Since the 128a popc is
already Simulated for 1600 ps, i haven't done membrane only simulation. So
i directly aligned my protein with the membrane using VMD and have saved
the coordinates. However after i aligned my protein with the membrane, i
felt the membrane was not big enough for my protein of interest, also, the
N-terminal region and the loop regions in the C-terminal region and
stretching outside water molecule above and below respectively.ow, i have
two questions here...


Yep, if the protein is sticking "out" of the box on both sides, the box is too 
small.



1. How would i increase the number of lipids from the existing one?


Two options:

1. genconf -nbox will give integer multiples of the lipid system (i.e., -nbox 2 
2 1 will expand the bilayer in the x and y directions and give 512 lipids)


2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit finer 
control over how large the box is and how many lipids will result.



2. Also, i should increase increase the number of water molecules above
and below the membrane so that it covers the whole region of N-terminal
and also the loop regions of the C-terminal.


Expand the box using editconf and add solvent with genbox.


Now, How to perform these tasks??If i do so will it be compatible with the
popc.itp file which i downloaded from the Prof. Tieleman's group?



None of the above operations have any influence on the parameters contained in 
popc.itp.  If you are unsure about Gromacs workflows, file formats, etc. then 
you really need read the manual and do some more basic tutorial material before 
you attempt a difficult simulation like a membrane protein.  There are a lot of 
pitfalls in simulating such a complex system, and if you are not ready for them, 
then you can waste a whole lot of time generating nonsensical results :)



3. My third question is while aligning my protein with the membrane should
i make a hole first or after aligning the protein should i remove the
overlapping lipids with the proteins?which one would be better??



There are several methods for doing this.  See below.


I have tried out some of the methodologies available in the internet but
it dosen't help me.If anyone of you have a detailed step by step
methodology right from the first step to till running the MD simulation
please let me know.


Saying you've tried things and they didn't work is useless.  What did you try? 
What links can you provide?  Have you tried the membrane protein tutorial linked 
from the Gromacs site?  That's about as step-by-step as it gets.


-Justin


Your help will be highly appreciated.
Looking forward to hear from you.

Best regards
Padmanabhan



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] POPC number

[Jochen Hub]

[EMAIL PROTECTED] wrote:
>> I guess that depends on the size of your protein. You should have enough
>> lipds such that the protein doesn't interact with its preriodic image.
>> 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
>> usually had something like 270 POPE molecules, but if you simulate a
>> smaller protein, less lipids may be sufficient. You may also want to use
>> a hexagonal box which will allow you have less lipids and water.
> 
> A hexagonal box? Great. How does one go about constructing that? Is this
> a cylinder-like box with hexagonal shape or just a triclinic one? In the
> triclinic case, does the PBC membrane turn out as it should?

And yes, the PBCs work just fine, as expected from any triclinic box.

cheer, jochen

> 
> Thanks,
> Chris.
> 
> 
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> 


-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] POPC number

[Jochen Hub]

[EMAIL PROTECTED] wrote:
>> I guess that depends on the size of your protein. You should have enough
>> lipds such that the protein doesn't interact with its preriodic image.
>> 90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
>> usually had something like 270 POPE molecules, but if you simulate a
>> smaller protein, less lipids may be sufficient. You may also want to use
>> a hexagonal box which will allow you have less lipids and water.
> 
> A hexagonal box? Great. How does one go about constructing that? Is this
> a cylinder-like box with hexagonal shape or just a triclinic one? In the
> triclinic case, does the PBC membrane turn out as it should?

Hey Chris,

a hexagonal box is a special case of a triclinic one: Here we go:

echo "CRYST1  90.0  90.0   40.00  90.00  90.00  60.0 P 1   1" >
x.pdb
genbox -cp x.pdb -cs tip4p -o filled.pdb
echo 0|trjconv -f filled.pdb -o compact.pdb -ur compact -s filled.pdb
pymol compact.pdb

Have fun,
Jochen



> 
> Thanks,
> Chris.
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] POPC number

[Jochen Hub]

I guess that depends on the size of your protein. You should have enough
 lipds such that the protein doesn't interact with its preriodic image.
90 POPC seem to be a bit to few for that. In my aquaporin simulations, I
usually had something like 270 POPE molecules, but if you simulate a
smaller protein, less lipids may be sufficient. You may also want to use
a hexagonal box which will allow you have less lipids and water.

cheers, jochen

sudheer babu wrote:
> Hi gmx-users,
> whats the number of POPC molecules should be there after inserting protein
> into popc? In my case 90 popc molecules are there around the protein from
> 128 molecues which I downloaded from Dr.Tielman's website.
> 
> Any suggestion will be appreciated
> Thanks in advance.
> 
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] POPC structure

[Justin A. Lemkul]

You can use genconf to replicate the 128-lipid system any number of 
times you wish.  You can also generate replicates of a subset of these 
lipids (say if you wanted to replicate only 100 of them) by identifying 
which residues you want, using genconf, and equilibrating thoroughly.


A similar discussion came across the list about a week ago...(hint: 
check the archives for stuff like this)


-Justin

minnale wrote:


 
Hi all,
  I found 128 popc lipid molecules in prof Tieleman's website ,I 
want to work on lipids with more than 128 popc lipid molecules, I knew 
that with help of VMD generate popc lipid molecules how many number we 
want. Can anyone suggest anyother website.


Thanks in advance.





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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] popc

[Justin A. Lemkul]

Quoting Chiara Parravicini <[EMAIL PROTECTED]>:

> Thank you for your advice!
> I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about
> the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and
> probably it would complain also for ffG43a2x-c.tdb. Here, also the fields
> gd_* don't match.  Is there the way to use the existing topologies with
> another gromos force field instead of reformatting all the ffG43a2x* files?

I wouldn't expect the gd_* to match between ffG53a6 and ffG43a2x, since ffG43a2x
was likely developed before ffG53a6 (hence the numbering).  If you have a look
at ffG43a1-c.tdb, you'll notice that the bonded parameters are comparable.

I would imagine that if the .hdb file was formatted in such a way that it can no
longer be used, I would suspect the .tdb files would suffer the same
consequences.  My first reaction is that the .tdb and .hdb files will be the
only ones that have to be re-formatted, however, I could be wrong.

You could probably start over with any of the other Gromos force fields if you'd
like, although I don't think the re-formatting would take too much time.

> What about the "atomtype 'CA' not found!" error?

There are several discussions about such things in the list archive.  If you
search for your error in conjunction with terms like "lipid," "membrane," etc.
you should turn up some results about how to deal with it.

-Justin

>
> On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
> > Quoting Chiara Parravicini <[EMAIL PROTECTED]>:
> >
> > > Dear gromacs users,
> > >
> > >  I would like to perform  simulations of a protein embedded in popc,
> > using a
> > > force field of the gromos series and I downloaded popc.pdb, popc.itp,
> > > lipid.itpa and the force field ffG43a2x extended for lipids.
> > > Looking throughout the archive I found different suggestions, but none
> > of
> > > them help me to successfully perform my simulations:
> > >
> > > - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I
> > get
> > > this error:
> > >
> > >  Fatal error:
> > >
> > > Error in hdb file ffG43a2x.hdb:
> > >
> > > Wrong number of control atoms (2 iso 3) on line:
> > >
> > > 1 1 N -C CA
> >
> > Right; I think the format of the .hdb file changed somewhere along the
> > way, and
> > ffG43a2x is formatted in the old style.  What pdb2gmx is complaining about
> > is
> > that it thinks it is trying to add an atom named 'N', with reference atoms
> > of
> > -C and CA.  Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will
> > see
> > the difference.  The first atom specified must be the name of the hydrogen
> > atom
> > you wish to add, so that line should be something like:
> >
> > 1   1   H   N   -C   CA
> >
> > For more on .hdb files, read the manual, section 5.5.2.
> >
> > -Justin
> >
> > >
> > >   - If I manually write a topology file for the ffG43a2x force field and
> > > submit it to grompp to write a .tpr, I get this error:
> > >
> > >  Fatal error:
> > > Atomtype 'CA' not found!
> > >
> > >   In the topology file I included both lipid.itp and popc.itp, and I
> > > commented the following lines in the lipid.itp file as suggested:
> > >
> > >  [ defaults ]
> > >
> > > 1 1
> > >
> > >  - I also tried to add the different sections [ atomtypes ], [ pairtypes
> > ],
> > > etc... of the lipid.itp files to ffG53a5* files, but I still get the
> > error:
> > >
> > >  Atomtype 'CA' not found!
> > >
> > >  Does anybody know what I miss? Is there a way to resolve this problem
> > and
> > > use popc with ffG53a5 or ffG43a2x?
> > >
> > >  All comments are very appreciated!
> > > Thanks in advance!
> > >
> > >  Chiara
> > >
> >
> >
> >
> > 
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > [EMAIL PROTECTED] | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > 
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to [EMAIL PROTECTED]
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> >
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] popc

[Chiara Parravicini]

Thank you for your advice!
I reformatted the ffG43a2x.hdb file, but now pdb2gmx is complaining about
the ffG43a2x-n.tdb file, that is different from the ffG53a6 one, and
probably it would complain also for ffG43a2x-c.tdb. Here, also the fields
gd_* don't match.  Is there the way to use the existing topologies with
another gromos force field instead of reformatting all the ffG43a2x* files?
What about the "atomtype 'CA' not found!" error?

On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> Quoting Chiara Parravicini <[EMAIL PROTECTED]>:
>
> > Dear gromacs users,
> >
> >  I would like to perform  simulations of a protein embedded in popc,
> using a
> > force field of the gromos series and I downloaded popc.pdb, popc.itp,
> > lipid.itpa and the force field ffG43a2x extended for lipids.
> > Looking throughout the archive I found different suggestions, but none
> of
> > them help me to successfully perform my simulations:
> >
> > - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I
> get
> > this error:
> >
> >  Fatal error:
> >
> > Error in hdb file ffG43a2x.hdb:
> >
> > Wrong number of control atoms (2 iso 3) on line:
> >
> > 1 1 N -C CA
>
> Right; I think the format of the .hdb file changed somewhere along the
> way, and
> ffG43a2x is formatted in the old style.  What pdb2gmx is complaining about
> is
> that it thinks it is trying to add an atom named 'N', with reference atoms
> of
> -C and CA.  Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will
> see
> the difference.  The first atom specified must be the name of the hydrogen
> atom
> you wish to add, so that line should be something like:
>
> 1   1   H   N   -C   CA
>
> For more on .hdb files, read the manual, section 5.5.2.
>
> -Justin
>
> >
> >   - If I manually write a topology file for the ffG43a2x force field and
> > submit it to grompp to write a .tpr, I get this error:
> >
> >  Fatal error:
> > Atomtype 'CA' not found!
> >
> >   In the topology file I included both lipid.itp and popc.itp, and I
> > commented the following lines in the lipid.itp file as suggested:
> >
> >  [ defaults ]
> >
> > 1 1
> >
> >  - I also tried to add the different sections [ atomtypes ], [ pairtypes
> ],
> > etc... of the lipid.itp files to ffG53a5* files, but I still get the
> error:
> >
> >  Atomtype 'CA' not found!
> >
> >  Does anybody know what I miss? Is there a way to resolve this problem
> and
> > use popc with ffG53a5 or ffG43a2x?
> >
> >  All comments are very appreciated!
> > Thanks in advance!
> >
> >  Chiara
> >
>
>
>
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> [EMAIL PROTECTED] | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
> 
> ___
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Re: [gmx-users] popc

[Justin A. Lemkul]

Quoting Chiara Parravicini <[EMAIL PROTECTED]>:

> Dear gromacs users,
>
>  I would like to perform  simulations of a protein embedded in popc, using a
> force field of the gromos series and I downloaded popc.pdb, popc.itp,
> lipid.itpa and the force field ffG43a2x extended for lipids.
> Looking throughout the archive I found different suggestions, but none of
> them help me to successfully perform my simulations:
>
> - Using the ffG43a2x* force field, when I run pdb2gmx on the popc.pdb, I get
> this error:
>
>  Fatal error:
>
> Error in hdb file ffG43a2x.hdb:
>
> Wrong number of control atoms (2 iso 3) on line:
>
> 1 1 N -C CA

Right; I think the format of the .hdb file changed somewhere along the way, and
ffG43a2x is formatted in the old style.  What pdb2gmx is complaining about is
that it thinks it is trying to add an atom named 'N', with reference atoms of
-C and CA.  Compare the ffG43a2x.hdb with, say, ffG53a6.hdb, and you will see
the difference.  The first atom specified must be the name of the hydrogen atom
you wish to add, so that line should be something like:

1   1   H   N   -C   CA

For more on .hdb files, read the manual, section 5.5.2.

-Justin

>
>   - If I manually write a topology file for the ffG43a2x force field and
> submit it to grompp to write a .tpr, I get this error:
>
>  Fatal error:
> Atomtype 'CA' not found!
>
>   In the topology file I included both lipid.itp and popc.itp, and I
> commented the following lines in the lipid.itp file as suggested:
>
>  [ defaults ]
>
> 1 1
>
>  - I also tried to add the different sections [ atomtypes ], [ pairtypes ],
> etc... of the lipid.itp files to ffG53a5* files, but I still get the error:
>
>  Atomtype 'CA' not found!
>
>  Does anybody know what I miss? Is there a way to resolve this problem and
> use popc with ffG53a5 or ffG43a2x?
>
>  All comments are very appreciated!
> Thanks in advance!
>
>  Chiara
>





Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/


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Re: [gmx-users] POPC simulation

[Marc F. Lensink]

On Thu, Nov 01, 2007 at 12:36:33PM +, Moutusi Manna wrote:
> Hi
>   I want to perform   peptide + popc membrane simulation. I download 
> popc128a.pdb from
>   (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
>   Before I introduce the peptide into the membrane, the water layer had to be 
> broadened to ensure full solvation of the peptide .I increase the water layer 
> using the following commands
>   1. editconf  -f  popc128a.pdb  -o  po_box.pdb  -box  6.1065  6.1059  9. 
>  -c
>   2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
>
>   Now, the no. of water molecules over the bilayer  increased . But, the 
> problem is that  there are water molecules inside the bilayer, which were 
> absent incase of popc128a.pdb. How can I remove these offending water 
> molecules?

calculate the average z position of the phosphorus atoms of both
layers, then remove all water molecules - of the just added set! -
that lie in between.

cheers,
marc


-- 
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Centre for Structural Biology and Bioinformatics SCMBB
Université Libre de Bruxelles  [EMAIL PROTECTED]
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tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425
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Re: [gmx-users] POPC simulation

[Mark Abraham]

[EMAIL PROTECTED] wrote:

Hi
  I want to perform   peptide + popc membrane simulation. I download 
 popc128a.pdb from
  
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
  Before I introduce the peptide into the membrane, the water layer  
had to be broadened to ensure full solvation of the peptide .I  
increase the water layer using the following commands
  1. editconf  -f  popc128a.pdb  -o  po_box.pdb  -box  6.1065   
6.1059  9.  -c

  2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top

  Now, the no. of water molecules over the bilayer  increased . But, 
 the problem is that  there are water molecules inside the bilayer,  
which were absent incase of popc128a.pdb. How can I remove these  
offending water molecules?




Did you search?

Search "water membrane" = first hit:
http://www.gromacs.org/pipermail/gmx-users/2007-March/026289.html

I and others also answered this question one week ago. Here is some info 
from that:

http://www.gromacs.org/pipermail/gmx-users/2007-October/030361.html
http://www.gromacs.org/pipermail/gmx-users/2007-October/030400.html

This probable deserves a wiki entry.


Done... http://wiki.gromacs.org/index.php/Membrane_Simulations
Someone who actually does this sort of simulation should check it over 
and expand as appropriate. Chris? Tsjerk?


Mark
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Re: [gmx-users] POPC simulation

[Justin A. Lemkul]

Quoting Moutusi Manna <[EMAIL PROTECTED]>:

>   thanks for reply.I want to perform simulation of popc membrane.
>   Steps which i have done are as follows:
>   1. download popc128a.pdb, popc.it,lipids.itp
>   (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
>   2. download ffgmx_lipids files
>   3.convert POPC of .top & popc.itp into POP as in popc.gro
>   4. #include "ffgmx.itp"
>   #include "lipid.itp"
>   #include "popc.itp"
>   #include "ffgmxnb.itp"
>   #include "ffgmxbon.itp"

These last two lines should already be included in ffgmx.itp, and including them
twice may cause some headaches.

>    in my .top file.
>
>   Now when I perform
>   pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top
>   it shows the error that"Residue 'POP' not found in residue topology
> database".
>   I think that's because of the fact that ffgmx.rtp do not
>   contain "POP" residue ,but it has DPPC residue.
>   Plz suggest how can i solve this problem.
>   thanks.

Use editconf to convert between .pdb and .gro.  You only need pdb2gmx if you
don't have a .top file, but Prof. Tieleman has kindly provided this for you
already, in the form of lipid.itp and popc.itp.

-Justin


==

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

==
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Re: [gmx-users] POPC membrane simulations

[Chris Neale]

I didn't realize that DPPC was available from the G53a5 force field. Probably 
you should find out how that was parameterized first (You could start by 
looking at the paper that published G53a5 or find a paper when somebody 
expanded that ff to include DPPC). You would then have the information that you 
need to create your own POPC. I would not recommend that you do this via 
pdb2gmx. Instead, take the dppc.itp that you already have (Hopefully you have 
one that is included in a .top file instead of a .top file that is full of 
hundreds of copies what could be .itp parameters... if not then I would 
generate a 1 molecule dmpc.itp first, include it in a .top and run your dppc 
simulation to be sure that you have done it correctly).

While the modification of dppc.itp to popc.itp seems relatively simple, the 
double bond makes it more difficult. Take a look at how this in handled in the 
charm lipids and in tieleman's parameters. I have previously posted to this 
list about not understanding the way that Tieleman's parameters handle the 
double bond (specifically the pairs around the double bond in the middle of RB 
dihedrals)
http://www.gromacs.org/pipermail/gmx-users/2006-September/023630.html
and an excerpt from another post of mine:
"I have yet to figure out exactly why things are 
treated as they are in the [ pairs ] section for two non-RB double-bonded 
carbons in the middle of a long chain of RB carbons :: more specifically I am 
referring to lipid acyl chains with a double bond (for example pope.itp from Dr. 
Tieleman)."
Unfortunately the CHARMM ff probably won't help you here as I doubt that it uses the RB dihedrals. 


Once you have the .itp file you will need to add a few parameter definitions at 
the top (the ones that aren't covered in ffG53a5bon.itp and ffG53a5nb.itp. I 
don't know what they are but you should easily determine this. Don't take those 
values directly from Tieleman's parameters -- his are probably from an earlier 
version of gromos. Again, refer to the original papers and then use ffG53a5 as 
a source for the parameters.

I have created new lipids (based on the ones from Tieleman's site, but all I 
have personally done is shorten or lengthen chains or change a choline to an 
ethanolamine. Introducing a double bond is significantly more difficult and I 
can make no claim that what I have suggested here is complete. It's my best 
first thoughts on the topic. Probably the rest is up to you. However, this list 
would benefit if you would post your procedure upon completion so that others 
with similar questions in the future could be guided by your work.
Chris.

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Re: [gmx-users] POPC membrane simulations

[maite lopez]

Hi Chris:

I´ve created my own dppc.itp using the ffG53a5 force field. I did that
running  only a dppc lipid of the membrane that is available on
Tieleman's site and i included it on my topology file and of course
put in it the number of dppc molecules . i haven´t had any problem
with this simulation. I didn´t use the dppc.itp of the Tieleman's
site.

But the topology of the popc isn´t on the gromacs database, for this i
can´t do the same. How the difference between dppc and popc lipids are
few  atoms in the oleoyl chain i thougth i could to converter my own
only_a_lipid_dppc.itp file into popc.itp file. That´s why the popc.itp
file of the Tieleman's site was done with ffgmx force field.

I think that i can to use the lipid.itp of the Tieleman's site and to
converter it  into ffG53a5 force field how you explain me. But my
question is :
Can i to obtain  my own  only_a_lipid_popc.itp file from my dppc.itp
and do the same such as my dppc simulation?
How could i do this?

Cheers,
Maite



On 3/22/07, Chris Neale <[EMAIL PROTECTED]> wrote:
If I understand correctly you want to construct popc.itp from the

dppc.itp that is available on Tieleman's site? And you have used PRODRG
to do this? That sounds like a lot of extra work when popc.itp is
directly available from Tieleman's site...
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

The fact that you want to use ffG53a5 and not ffgmx is more of an issue.
To do that you need to avoid lipid.itp and do something like this:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
However, you will want to heed this warning (or at least understand it):
http://www.gromacs.org/pipermail/gmx-users/2006-September/023640.html

Chris.

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Re: [gmx-users] POPC simulation

[Venky Krishna]

Hi all,I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. Renaming of POP to POPC in the .gro files doesn't matter... the main thing is to change the [Defaults] in the lipid.itp file (this eliminates the LC3 atomtype not found error)my .top files and modified lipid.itp files look like.---grompp.top--#include "ffgmx.itp"#include "lipid.itp"#include "popc.itp"#include "protein.top"#include "spin.top"#include "ions.itp"#ifdef FLEX_SPC	; removed these following lines from the protein.top file and appended into one single .top file.#include "flexspc.itp"#else#include "spc.itp"#endif#ifdef POSRES_WATER; Position restraint for each water oxygen[ position_restraints ];  i funct       fcx        fcy        fcz   1    1       1000       1000       1000#endif[ system ]; nameBR_103C[ molecules ]; name	numberProtein 	1DRG		1POPC		154SOL     	13393---lipid.itp (notice the defaults directive is commented out... this eliminates the AtomType 'LC3' not found error)-;; this forcefield is a mixture of lipid and GROMOS parameters. GROMOS;; parameters taken from ffgmxnb.itp, lipid parameters from Berger et;; al, Biophys. J. 72, pp. 2002-2013. Parameters starting with L are;; lipid parameter. LP2 and LP3 are Bergers pentadecane parameters,;; the rest is OPLS. The lipids see SPC/SPCE, and lipids as;; OPLS/Berger, protein as GROMOS, the protein sees lipids as GROMOS. ;[ defaults ];1       1[ atomtypes ];name     mass     charge ptype  c6           c12;   LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS  LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS  LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS   LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS  LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS  LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS   LP    30.9738    0.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS  LOS    15.9994    0.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS  LP2    14.0270    0.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ  LP3    15.0350    0.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ  LC3    15.0350    0.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS  LC2    14.0270    0.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLScontd...---That is all the modifications required for running the simulation. Hope this helps people with similar problem in the future.Venks Venky KrishnamaniDr.Janos K. Lanyi Lab,D320, Medical Sciences DUniversity of California, Irvine On May 29, 2006, at 12:23 PM, Arindam Ganguly wrote:Hi All,thanks to Steffan , Jim and Kaushal for helping me out in the POPC simulation setup. i finally got everything to work. i guess the imp thing was to change the POPC to POP in .top file. thanks once again.Arindam Ganguly ___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___
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Re: [gmx-users] POPC simulation

[Jim Fonseca]

ent-Type: text/plain; charset=us-ascii

Mark Abraham <[EMAIL PROTECTED]> writes:

>
> David van der Spoel wrote:
> > Gale, Ella wrote:
> >
> >>
> >> Thanks for the advice, but my force-field has no charges and  
hence no
> >> coulomb potential, so I want the atoms to interact with  
itself via the
> >> Van der Waals functions. I'm using 3.2.1 at the moment and  
there is no
> >> option to use any of the Ewald summation techniques. Is this  
something

> >> that has been added in the most recent version?
> >
> > Ewald variant are only for Coulomb so far. You can use a  
normal cutoff

> > or a shifted cutoff.
>
> One or two of the early PME papers describe implementation  
details for

> LJ PME, but I am not immediately aware of a modern MD code that
> implements it. If you want it, shop around.
>
> Mark
>
I got to read a note by Cheatham on PME for LJ VDW.
Look for question "Is there a PME algorithm also for the VDW  
interactions?"

in

http://amber.scripps.edu/Questions/ewald.html

Yang Ye





--

Message: 8
Date: Wed, 24 May 2006 14:39:10 -0400
From: Jim Fonseca <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] POPC simulation
To: Discussion list for GROMACS users 
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Arindam,
I fixed this problem a while ago and it was pretty difficult to
figure out.  I tinkered with so many things, once I got it to work I
didn't even know what steps I took to fix it!

Here's something to try:  GROMACS doesn't like the fact popc.itp has
a four-character residue name (since protein residues are just three
characters).  If you look at your .gro file, you'll probably see that
somewhere along the line, the POPC got truncated to POP.  Try
changing all instances of 'POPC' to 'POP' in your setup--this should
probably just be in popc.itp (lots of occurrences) and topol.top(one
occurrence where you list the number of POP molecules.

Please let me know if that works.

Jim

On May 24, 2006, at 1:02 PM, Arindam Ganguly wrote:

> Hi Steffen,
> thanks for the reply. this is what i have done. my topol.top looks
> like this now
> #inlcude ffgmx.itp
> inlcude popc.itp.
>
> as per your last reply i have copied the contents of lipid.itp to
> ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
> respective file. basically just appended the files with the  
contents

> of the lipid.itp .
>
> now when i run grommp -v - -f em.mdp ,
> it still says atom type "LC3" not found,.
>
> i can't understand why this mistake in fact taking place. popc.itp
> file the first 3 lines after [atom]
> in fact mentions LC3. so where is the mistake. plx help. thanks.
> arindam
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Re: [gmx-users] POPC simulation

[Jim Fonseca]

Arindam,
I fixed this problem a while ago and it was pretty difficult to  
figure out.  I tinkered with so many things, once I got it to work I  
didn't even know what steps I took to fix it!


Here's something to try:  GROMACS doesn't like the fact popc.itp has  
a four-character residue name (since protein residues are just three  
characters).  If you look at your .gro file, you'll probably see that  
somewhere along the line, the POPC got truncated to POP.  Try  
changing all instances of 'POPC' to 'POP' in your setup--this should  
probably just be in popc.itp (lots of occurrences) and topol.top(one  
occurrence where you list the number of POP molecules.


Please let me know if that works.

Jim

On May 24, 2006, at 1:02 PM, Arindam Ganguly wrote:


Hi Steffen,
thanks for the reply. this is what i have done. my topol.top looks
like this now
#inlcude ffgmx.itp
inlcude popc.itp.

as per your last reply i have copied the contents of lipid.itp to
ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
respective file. basically just appended the files with the contents
of the lipid.itp .

now when i run grommp -v - -f em.mdp ,
it still says atom type "LC3" not found,.

i can't understand why this mistake in fact taking place. popc.itp
file the first 3 lines after [atom]
in fact mentions LC3. so where is the mistake. plx help. thanks.
arindam
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Re: [gmx-users] POPC simulation

[Steffen Wolf]

Arindam Ganguly wrote:

Hi Steffen,
Thanks very much for the prompt reply. i made the changes as mentioned 
such that my popc.top looks like this :-

#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "ffgmx2nb.itp"
#include "ffgmx2bon.itp"

however is still get the same message "Fatal error: Bonded/nonbonded 
atom type 'LP2' not found!". 
i forgot to mention one thing in my earlier mail that the ffgmx.atp 
file provided with originally from GROMACS , i replaced the contents 
of it by the contents present in the ffgmx.atp file present in the 
ffgmx_lipids folder as downloaded from the Gromacs website.
 

my understanding is this shouldn;t cause the problem since the 
orinigal ffgmx.atp file ( as provided by gromacs) doesn;t contain all 
the atom types. in fact when i compared the both files i found that 
the ffgmx.atp file (from ffgmx_lipids folder ) has the following extra 
entries which were required for the lipid simulation. i am kind of 
confused as to where i am committig the mistake. plz help. thanks.


Arindam Ganguly

Hm, strange, but OK, another idea: I just saw that your setup 
essentially trippels the callups for the necessary forcefield 
parameters: You can not only transfer the atomtypes to ffgmxbon.itp, but 
the rest of the included parameters into ffgmxbon.itp and ffgmxnb.itp as 
well, so you won't have to call lipid.itp. Next thing: why are you 
including ffgmx2nb.itp and ffgmx2bon.itp explicitly? They are already 
set up by calling ffgmx.itp in the beginning, you're just overriding 
everything again. So: after modifying lipid.itp, you should do fine with

#include "ffgmx.itp"
#include "popc.itp"
Bye
Steffen
--
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: [EMAIL PROTECTED]
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Re: [gmx-users] POPC simulation

[Steffen Wolf]

Hi Arindam,
you've simply got to switch two lines in the *.top file: lipid.itp has 
to be called by the topology before popc.itp, as it contains the 
information on atomtypes for GROMACS. So:


#include "lipid.itp"
#include "popc.itp"

should work just fine.
Greetings
Steffen

--
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Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: [EMAIL PROTECTED]
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Re: [gmx-users] popc

[Itamar Kass]

Shalom,


Try "make_hole.pl -f "input".pdb -o "output".pdb -r 1.2 -lipat P -lipid POP"


Itamar


P.S. look at the pdb file for the atom name of the phosphate atom. I use 
DMPC so it is P, but it is also might be P8 or such.






MGiò wrote:


Ooops!
I mean, I'm using popc.itp, of course!
bye,
MG

On 5/2/06, *MGiò* <[EMAIL PROTECTED] > wrote:

Hi!
I'm using the popc.top which I have downloaded from this website
http://moose.bio.ucalgary.ca/index.php?page=Downloads
and the forcefield I'm using is ffgmx, gromacs forcefield.

Cheers,
MG


On 5/2/06, *mahbubeh zarrabi* < [EMAIL PROTECTED]
> wrote:

hi
I try to use make_hole program to make a hole in POPC.
how can i make popc.top?what is forcefield for popc in
gromacs?
thanks
zarrabi


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Re: [gmx-users] popc

[MGiò]

Ooops!I mean, I'm using popc.itp, of course!bye,MGOn 5/2/06, MGiò <[EMAIL PROTECTED]> wrote:
Hi!I'm using the popc.top which I have downloaded from this website
http://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield.
Cheers,MGOn 5/2/06, mahbubeh zarrabi <
[EMAIL PROTECTED]> wrote:
 hiI try to use make_hole program to make a hole in POPC.how can i make popc.top?what is forcefield for popc ingromacs?thankszarrabi__Do You Yahoo!?
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Re: [gmx-users] popc

[MGiò]

Hi!I'm using the popc.top which I have downloaded from this websitehttp://moose.bio.ucalgary.ca/index.php?page=Downloadsand the forcefield I'm using is ffgmx, gromacs forcefield.
Cheers,MGOn 5/2/06, mahbubeh zarrabi <[EMAIL PROTECTED]> wrote:
 hiI try to use make_hole program to make a hole in POPC.how can i make popc.top?what is forcefield for popc ingromacs?thankszarrabi__Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection aroundhttp://mail.yahoo.com___gmx-users mailing list
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