Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

2019-06-15 Thread Justin Lemkul 



On 6/15/19 8:56 AM, paul buscemi wrote:

The pressure on a (real-life)  membrane is not isotropic, edges are under 
tension. so using the p-couple “surface-tension”  - with water layers is 
appropriate.


Applying surface tension and semiisotropic coupling will result in 
different ensembles. The former yields NPgammaT, the latter NPT. 
Semiisotropic pressure coupling is the de facto standard in modern 
membrane simulations unless an additional surface tension is necessary.


-Justin


If you use p-couple  = isotropic  you should end up with a micelle because the 
hydrophobic effects are significant.


p


On Jun 14, 2019, at 11:18 PM, Prasanth G, Research Scholar 
 wrote:

Dear Bratin,

When I am using a semiisotropic condition the pbc box is
deforming/compressing pushing the lipid bilayer apart. I am attaching the
screenshots of the system at the beginning(normal.png) of production run as
well as at the end of 30ns simulation (elongated.png) for your reference.

This was my production mdp (md.mdp) file:

title   = pro-DPP-LIG  Production MD
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1500; 2 * 1500 = 3 ps (1 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstxtcout   = 1000  ; xtc compressed trajectory output every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation= yes   ; Restarting after NPT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps = Protein_LIG_DPP   Water_and_ions  ;
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 323   323 ; reference temperature, one
for each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_LIG_DPP  Water_and_ions
---
*LIG is ligand and
DPP is DPPC.

Thank you.

normal.png


elongated.png


On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:


Dear all,

Can someone please tell me if it is okay to use isotropic pcoupltype for a
membrane protein simulation? Are there any disadvantages?

Also, why is semiisotropic preferred over isotropic, in membrane protein
simulations..

Thank you.
--
Regards,
Prasanth.



--
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Prasanth.
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Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

2019-06-15 Thread paul buscemi 
The pressure on a (real-life)  membrane is not isotropic, edges are under 
tension. so using the p-couple “surface-tension”  - with water layers is 
appropriate. 

If you use p-couple  = isotropic  you should end up with a micelle because the 
hydrophobic effects are significant.


p

> On Jun 14, 2019, at 11:18 PM, Prasanth G, Research Scholar 
>  wrote:
> 
> Dear Bratin,
> 
> When I am using a semiisotropic condition the pbc box is
> deforming/compressing pushing the lipid bilayer apart. I am attaching the
> screenshots of the system at the beginning(normal.png) of production run as
> well as at the end of 30ns simulation (elongated.png) for your reference.
> 
> This was my production mdp (md.mdp) file:
> 
> title   = pro-DPP-LIG  Production MD
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 1500; 2 * 1500 = 3 ps (1 ns)
> dt  = 0.002 ; 2 fs
> ; Output control
> nstxout = 1000  ; save coordinates every 2 ps
> nstvout = 1000  ; save velocities every 2 ps
> nstxtcout   = 1000  ; xtc compressed trajectory output every 2 ps
> nstenergy   = 1000  ; save energies every 2 ps
> nstlog  = 1000  ; update log file every 2 ps
> ; Bond parameters
> continuation= yes   ; Restarting after NPT
> constraint_algorithm= lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cels
> nstlist = 5 ; 10 fs
> rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
> rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
> rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
> pme_order   = 4 ; cubic interpolation
> fourierspacing  = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl  = Nose-Hoover   ; More accurate thermostat
> tc-grps = Protein_LIG_DPP   Water_and_ions  ;
> tau_t   = 0.5   0.5 ; time constant, in ps
> ref_t   = 323   323 ; reference temperature, one
> for each group, in K
> ; Pressure coupling is on
> pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
> independent z
> tau_p   = 2.0   ; time constant, in ps
> ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no; Velocity generation is off
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode   = Linear
> comm-grps   = Protein_LIG_DPP  Water_and_ions
> ---
> *LIG is ligand and
> DPP is DPPC.
> 
> Thank you.
> 
> normal.png
> 
> 
> elongated.png
> 
> 
> On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar <
> prasanthgha...@sssihl.edu.in> wrote:
> 
>> Dear all,
>> 
>> Can someone please tell me if it is okay to use isotropic pcoupltype for a
>> membrane protein simulation? Are there any disadvantages?
>> 
>> Also, why is semiisotropic preferred over isotropic, in membrane protein
>> simulations..
>> 
>> Thank you.
>> --
>> Regards,
>> Prasanth.
>> 
> 
> 
> -- 
> Regards,
> Prasanth.
> -- 
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

2019-06-14 Thread Prasanth G, Research Scholar 
Dear Bratin,

When I am using a semiisotropic condition the pbc box is
deforming/compressing pushing the lipid bilayer apart. I am attaching the
screenshots of the system at the beginning(normal.png) of production run as
well as at the end of 30ns simulation (elongated.png) for your reference.

This was my production mdp (md.mdp) file:

title   = pro-DPP-LIG  Production MD
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 1500; 2 * 1500 = 3 ps (1 ns)
dt  = 0.002 ; 2 fs
; Output control
nstxout = 1000  ; save coordinates every 2 ps
nstvout = 1000  ; save velocities every 2 ps
nstxtcout   = 1000  ; xtc compressed trajectory output every 2 ps
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
; Bond parameters
continuation= yes   ; Restarting after NPT
constraint_algorithm= lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1.2   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.2   ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = Nose-Hoover   ; More accurate thermostat
tc-grps = Protein_LIG_DPP   Water_and_ions  ;
tau_t   = 0.5   0.5 ; time constant, in ps
ref_t   = 323   323 ; reference temperature, one
for each group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm = 1
comm-mode   = Linear
comm-grps   = Protein_LIG_DPP  Water_and_ions
---
*LIG is ligand and
DPP is DPPC.

Thank you.

 normal.png


 elongated.png


On Fri, Jun 14, 2019 at 12:09 PM Prasanth G, Research Scholar <
prasanthgha...@sssihl.edu.in> wrote:

> Dear all,
>
> Can someone please tell me if it is okay to use isotropic pcoupltype for a
> membrane protein simulation? Are there any disadvantages?
>
> Also, why is semiisotropic preferred over isotropic, in membrane protein
> simulations..
>
> Thank you.
> --
> Regards,
> Prasanth.
>


-- 
Regards,
Prasanth.
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Re: [gmx-users] Membrane protein simulation isotropic vs semiisotropic

2019-06-14 Thread Bratin Kumar Das 
Hi
Why you want to do isotropic?

On Fri 14 Jun, 2019, 12:16 PM Prasanth G, Research Scholar, <
prasanthgha...@sssihl.edu.in> wrote:

> Dear all,
>
> Can someone please tell me if it is okay to use isotropic pcoupltype for a
> membrane protein simulation? Are there any disadvantages?
>
> Also, why is semiisotropic preferred over isotropic, in membrane protein
> simulations..
>
> Thank you.
> --
> Regards,
> Prasanth.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] Membrane-protein Simulation

2019-05-06 Thread Justin Lemkul 


Please don't reply to the whole digest.

On 5/6/19 6:47 AM, Sankaran SV . wrote:

@email on Membrane protein Simulation:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html

Dear Najamuddin Memon

Thanks for your reply. I am a little confused here. Why is the protein
alone drifting? Typically, when we simulate protein only or protein-ligand
systems, the protein along with the co-molecule drifts – and hence we do
pbc correction. But in our case, we observed that the lipid does NOT move.
Only the protein, which is supposedly embedded in the lipid, drifts.


This is not true. Everything moves. Visualize any individual lipid and 
you will see it diffuse over time. Lipid diffusion timescales are 
extremely long, though, so net movement is much lower. But the protein 
is certainly capable of drifting (again, along with everything else) and 
is simply the most prominent species that is the most obvious to have 
changed its position.



Further, when we proceeded with centering the system with respect to the
protein (which removed the drift), and calculated the number of water
molecules that remained in the interface layer (defined as 4.5 angstrom
from the protein) throughout the simulation, the two numbers were
different. That is, we obtained 16 waters molecules that remained in the
interface layer BEFORE centering and only 5 were found to be in the
interface layer AFTER centering. Would centering affect the number of water
molecules that resides in the hydration layer throughout the simulation?


Centering doesn't affect anything, just visualization convention. You 
need to be sure you're performing a robust calculation, but you haven't 
shown us how you're doing it so it's not possible to give more precise 
advice.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Membrane-protein Simulation

2019-05-06 Thread Sankaran SV . 
> >
> > Group13 (T1P) has26 elements
> >
> > Group14 (S1P) has12 elements
> >
> > Group15 ( NA) has16 elements
> >
> > Group16 (  Water) has 40209 elements
> >
> > Group17 (SOL) has 40209 elements
> >
> > Group18 (  non-Water) has  2981 elements
> >
> > Group19 (Ion) has16 elements
> >
> > Group20 (T1P) has26 elements
> >
> > Group21 (S1P) has12 elements
> >
> > Group22 ( NA) has16 elements
> >
> > Group23 ( Water_and_ions) has 40225 elements
> >
> >
> > If i check for independent replica, using the below command
> >
> > echo 4 4 | gmx rms ?f 1_trj_50ps.xtc -s 1_trj.tpr -o 1_rmsd.xvg -tu ns
> >
> > Select group for output
> >
> > Group 0 ( System) has 43190 elements
> >
> > Group 1 (Protein) has  2965 elements
> >
> > Group 2 (  Protein-H) has  2334 elements
> >
> > Group 3 (C-alpha) has   295 elements
> >
> > Group 4 (   Backbone) has   885 elements
> >
> > Group 5 (  MainChain) has  1181 elements
> >
> > Group 6 (   MainChain+Cb) has  1458 elements
> >
> > Group 7 (MainChain+H) has  1469 elements
> >
> > Group 8 (  SideChain) has  1496 elements
> >
> > Group 9 (SideChain-H) has  1153 elements
> >
> > Group10 (Prot-Masses) has  2965 elements
> >
> > Group11 (non-Protein) has 40225 elements
> >
> > Group12 (  Other) has 40225 elements
> >
> > Group13 (SOL) has 40209 elements
> >
> > Group14 ( NA) has16 elements
> >
> > is it ok to make index file (protein+phosphoresidues) for analysis of the
> > concatenated trajectory.
> >
> > Please advise me
> >
> > Thanks a lot
> > Gosu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
>
>
> --
>
> Message: 2
> Date: Thu, 2 May 2019 15:40:49 +0500
> From: Najamuddin Memon 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Membrane-protein Simulation
> Message-ID:
>  p...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Yes it is normal to correct .xtc file through -pbc flag
>
> On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in>
> wrote:
>
> > Dear all,
> >
> > We are investigating the hydration dynamics of membrane proteins (AQP
> > embedded in DPPC membrane). The topology and the mdp files for
> simulations
> > was obtained from the MemprotMD database (mdp file:
> > http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of
> > simulation to 310 K since we are interested in the hydration dynamics at
> > body temperature. After 100 ns simulations, we observe that the protein
> has
> > drifted from the center of the bilayer to the periphery. There was no
> > changes in the lipid layers. The apparent movement of the protein
> vanished
> > after pbc correction was performed with centering the protein. Could you
> > please advise if it is common to observe proteins drifting during the
> > simulation and if it is fine to correct it with pbc correction?
> >
> > Thanks.
> > --
> > 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.
> >
>
>
> --
>
> Message: 3
> Date: Thu, 2 May 2019 16:29:57 +0530
> From: Saumyak Mukherjee 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] problem regarding gmx trjconv
> Message-ID:
> <
> cagctgrwfyshaacojmr3zmdjjoaspvwuprijoogeeemc+z+a...@mail.gmail.com>
> Conte

Re: [gmx-users] Membrane-protein Simulation

2019-05-02 Thread Najamuddin Memon 
Yes it is normal to correct .xtc file through -pbc flag

On Thu, May 2, 2019, 12:57 PM Sankaran SV . <119013...@sastra.ac.in> wrote:

> Dear all,
>
> We are investigating the hydration dynamics of membrane proteins (AQP
> embedded in DPPC membrane). The topology and the mdp files for simulations
> was obtained from the MemprotMD database (mdp file:
> http://memprotmd.bioch.ox.ac.uk/). We modified the temperature of
> simulation to 310 K since we are interested in the hydration dynamics at
> body temperature. After 100 ns simulations, we observe that the protein has
> drifted from the center of the bilayer to the periphery. There was no
> changes in the lipid layers. The apparent movement of the protein vanished
> after pbc correction was performed with centering the protein. Could you
> please advise if it is common to observe proteins drifting during the
> simulation and if it is fine to correct it with pbc correction?
>
> Thanks.
> --
> 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
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] membrane-protein simulation

2017-08-02 Thread Amir Zeb 
Thanks Justin

Got it, it's working.

On Wed, Aug 2, 2017 at 10:02 AM, Justin Lemkul  wrote:

>
>
> On 8/2/17 5:01 AM, Amir Zeb wrote:
>
>> Hello gmx-user
>>
>> I want to simulate a membrane protein with more than one chains like A, B,
>> C etc. I generated the strong_posre.itp  file as Justing has kindly
>> explained in his tutorial, and updated the topol.top file by inserting the
>> same lines. I also updated the minim.mdp file by inserting STRONG_POSRES.
>> Once I tried the minimization of the system before the shrinking step, I
>> got the error as below:
>>
>> Fatal error:
>> [ file strong_posre.itp, line 548 ]:
>> Atom index (544) in position_restraints out of bounds (1-543).
>> This probably means that you have inserted topology section
>> "position_restraints"
>> in a part belonging to a different molecule than you intended to.
>> In that case move the "position_restraints" section to the right molecule.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> I tried so many options but could not fix the issue. Please keep in view
>> that the same procedure is working well with a single chain of the
>> protein.
>> Kindly help me how to fix this issue?
>>
>>
> You need to create restraint files for each chain separately and include
> them in each [moleculetype] separately, as explained here:
>
> http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_
> position_restraints_out_of_bounds
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/Support
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Re: [gmx-users] membrane-protein simulation

2017-08-02 Thread Justin Lemkul 



On 8/2/17 5:01 AM, Amir Zeb wrote:

Hello gmx-user

I want to simulate a membrane protein with more than one chains like A, B,
C etc. I generated the strong_posre.itp  file as Justing has kindly
explained in his tutorial, and updated the topol.top file by inserting the
same lines. I also updated the minim.mdp file by inserting STRONG_POSRES.
Once I tried the minimization of the system before the shrinking step, I
got the error as below:

Fatal error:
[ file strong_posre.itp, line 548 ]:
Atom index (544) in position_restraints out of bounds (1-543).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I tried so many options but could not fix the issue. Please keep in view
that the same procedure is working well with a single chain of the protein.
Kindly help me how to fix this issue?



You need to create restraint files for each chain separately and include them in 
each [moleculetype] separately, as explained here:


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

-Justin

--
==

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

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

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

==
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Re: [gmx-users] membrane protein simulation

2015-09-13 Thread Brett 
Thanks for the reply Tsjerk. In fact I am just wonding if the situation exist, 
i.e., for the  10th trans-membrane helices in the protein, the 8th and or 9th 
for example is/are a little shorter than the other several helices. Will you 
please give a comment on how to process this kind of membrane protein embeding 
in lipid  Tsjerk?
 
Brett







At 2015-09-13 15:19:56, "Tsjerk Wassenaar"  wrote:
>Hi Brett,
>
>Say I'm designing this new type of truck. Because the earth  it's riding
>over is round, do you think I need to adjust the wheel positions on front
>and back to match the curvature of the earth?
>
>Cheers,
>
>Tsjerk
>On Sep 13, 2015 08:52, "Brett"  wrote:
>
>>
>> Dear All,
>>
>> Suppose a membrane protein contains 10 trans-membrane helix, and as the
>> cell membrane is round, the upper and lower part of the 10 trans- membrane
>> are not horizontal as they are part of the rounded cell, will you please
>> introduce to me how to make the lipid bilayer in curve to parallel the
>> upper and lower part of the 10 tran- membrane? I only know we can pack the
>> membrane protein into the lipid bilayer in the way the lipid bilayer would
>> be perpendicular to the membrane protein.
>>
>> Yesterday I have posted a similar question but my post was not show in the
>> post list.
>>
>> I am looking forward to getting your reply.
>>
>>
>> Best regards.
>>
>>
>> Brett
>>
>>
>>
>>
>>
>>
>>
>>
>>  Forwarding messages 
>> From: "Machtens, Jan-Philipp" 
>> Date: 2015-09-10 16:41:33
>> To:  "gromacs.org_gmx-users@maillist.sys.kth.se" <
>> gromacs.org_gmx-users@maillist.sys.kth.se>
>> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer
>> (martini)
>> Hi Kathrin,
>> if I remember correctly I once did something similar with g_membed -pieces
>> !
>>
>> Cheers,
>> 
>> Dr. Jan-Philipp Machtens
>> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
>> Forschungszentrum Jülich, Germany
>> Telefon:  02461 616467
>> 
>>
>> 
>> Date: Thu, 10 Sep 2015 01:25:00 +0200
>> From: Kathrin Hadasch 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: [gmx-users] Multiple membrane proteins in complex bilayer
>> (martini)
>> Message-ID: <55f0bfcc.7060...@web.de>
>> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>>
>> Hey you all,
>> I'm searching for a way to insert and embed multiple(!) copies of the
>> same protein in a complex, presimulated membrane patch (all martini-cg).
>> I've tryed lambada for insertion, but I couldn't get it to work with
>> more than one protein. I've tried to translate the protein to a (4 4 0)
>> vector with editconf in the lambada script, but I get following error:
>> Modification of non-creatable array value attempted, subscript -6 at
>> /home/lambada/modules/protein.pm line 281.
>> For insertion via vmd, I have no clue how to generate a psf file for
>> martini-lipids.
>> Any suggestions how I could make it work?
>> Best regards and thanks in advance,
>> Kathrin
>>
>>
>>
>> 
>>
>> 
>> Forschungszentrum Juelich GmbH
>> 52425 Juelich
>> Sitz der Gesellschaft: Juelich
>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> Prof. Dr. Sebastian M. Schmidt
>>
>> 
>>
>> 
>>
>> --
>> 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.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] membrane protein simulation

2015-09-13 Thread Tsjerk Wassenaar 
Hi Brett,

So apart from the curvature of the membrane, there maybe the situation that
there's just more of the protein in one leaflet than in the other. You'll
need to account for that when embedding. Membrane builders typically check
for overlaps to take care of this.

Cheers,

Tsjerk
On Sep 13, 2015 11:37, "Brett"  wrote:

> Thanks for the reply Tsjerk. In fact I am just wonding if the situation
> exist, i.e., for the  10th trans-membrane helices in the protein, the 8th
> and or 9th for example is/are a little shorter than the other several
> helices. Will you please give a comment on how to process this kind of
> membrane protein embeding in lipid  Tsjerk?
>
> Brett
>
>
>
>
>
>
>
> At 2015-09-13 15:19:56, "Tsjerk Wassenaar"  wrote:
> >Hi Brett,
> >
> >Say I'm designing this new type of truck. Because the earth  it's riding
> >over is round, do you think I need to adjust the wheel positions on front
> >and back to match the curvature of the earth?
> >
> >Cheers,
> >
> >Tsjerk
> >On Sep 13, 2015 08:52, "Brett"  wrote:
> >
> >>
> >> Dear All,
> >>
> >> Suppose a membrane protein contains 10 trans-membrane helix, and as the
> >> cell membrane is round, the upper and lower part of the 10 trans-
> membrane
> >> are not horizontal as they are part of the rounded cell, will you please
> >> introduce to me how to make the lipid bilayer in curve to parallel the
> >> upper and lower part of the 10 tran- membrane? I only know we can pack
> the
> >> membrane protein into the lipid bilayer in the way the lipid bilayer
> would
> >> be perpendicular to the membrane protein.
> >>
> >> Yesterday I have posted a similar question but my post was not show in
> the
> >> post list.
> >>
> >> I am looking forward to getting your reply.
> >>
> >>
> >> Best regards.
> >>
> >>
> >> Brett
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>  Forwarding messages 
> >> From: "Machtens, Jan-Philipp" 
> >> Date: 2015-09-10 16:41:33
> >> To:  "gromacs.org_gmx-users@maillist.sys.kth.se" <
> >> gromacs.org_gmx-users@maillist.sys.kth.se>
> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer
> >> (martini)
> >> Hi Kathrin,
> >> if I remember correctly I once did something similar with g_membed
> -pieces
> >> !
> >>
> >> Cheers,
> >> 
> >> Dr. Jan-Philipp Machtens
> >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
> >> Forschungszentrum Jülich, Germany
> >> Telefon:  02461 616467
> >> 
> >>
> >> 
> >> Date: Thu, 10 Sep 2015 01:25:00 +0200
> >> From: Kathrin Hadasch 
> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer
> >> (martini)
> >> Message-ID: <55f0bfcc.7060...@web.de>
> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
> >>
> >> Hey you all,
> >> I'm searching for a way to insert and embed multiple(!) copies of the
> >> same protein in a complex, presimulated membrane patch (all martini-cg).
> >> I've tryed lambada for insertion, but I couldn't get it to work with
> >> more than one protein. I've tried to translate the protein to a (4 4 0)
> >> vector with editconf in the lambada script, but I get following error:
> >> Modification of non-creatable array value attempted, subscript -6 at
> >> /home/lambada/modules/protein.pm line 281.
> >> For insertion via vmd, I have no clue how to generate a psf file for
> >> martini-lipids.
> >> Any suggestions how I could make it work?
> >> Best regards and thanks in advance,
> >> Kathrin
> >>
> >>
> >>
> >>
> 
> >>
> >>
> 
> >> Forschungszentrum Juelich GmbH
> >> 52425 Juelich
> >> Sitz der Gesellschaft: Juelich
> >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> >> Prof. Dr. Sebastian M. Schmidt
> >>
> >>
> 
> >>
> >>
> 
> >>
> >> --
> >> 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] membrane protein simulation

2015-09-13 Thread Brett 
Dear Tsjerk,
 
Thanks for the reply. Will you please introduce to me sevral membrane builders 
whith results compatible with gromacs, especially on-line available membrane 
builders?
 
Best regards.
 
Brett







At 2015-09-13 17:45:52, "Tsjerk Wassenaar"  wrote:
>Hi Brett,
>
>So apart from the curvature of the membrane, there maybe the situation that
>there's just more of the protein in one leaflet than in the other. You'll
>need to account for that when embedding. Membrane builders typically check
>for overlaps to take care of this.
>
>Cheers,
>
>Tsjerk
>On Sep 13, 2015 11:37, "Brett"  wrote:
>
>> Thanks for the reply Tsjerk. In fact I am just wonding if the situation
>> exist, i.e., for the  10th trans-membrane helices in the protein, the 8th
>> and or 9th for example is/are a little shorter than the other several
>> helices. Will you please give a comment on how to process this kind of
>> membrane protein embeding in lipid  Tsjerk?
>>
>> Brett
>>
>>
>>
>>
>>
>>
>>
>> At 2015-09-13 15:19:56, "Tsjerk Wassenaar"  wrote:
>> >Hi Brett,
>> >
>> >Say I'm designing this new type of truck. Because the earth  it's riding
>> >over is round, do you think I need to adjust the wheel positions on front
>> >and back to match the curvature of the earth?
>> >
>> >Cheers,
>> >
>> >Tsjerk
>> >On Sep 13, 2015 08:52, "Brett"  wrote:
>> >
>> >>
>> >> Dear All,
>> >>
>> >> Suppose a membrane protein contains 10 trans-membrane helix, and as the
>> >> cell membrane is round, the upper and lower part of the 10 trans-
>> membrane
>> >> are not horizontal as they are part of the rounded cell, will you please
>> >> introduce to me how to make the lipid bilayer in curve to parallel the
>> >> upper and lower part of the 10 tran- membrane? I only know we can pack
>> the
>> >> membrane protein into the lipid bilayer in the way the lipid bilayer
>> would
>> >> be perpendicular to the membrane protein.
>> >>
>> >> Yesterday I have posted a similar question but my post was not show in
>> the
>> >> post list.
>> >>
>> >> I am looking forward to getting your reply.
>> >>
>> >>
>> >> Best regards.
>> >>
>> >>
>> >> Brett
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>  Forwarding messages 
>> >> From: "Machtens, Jan-Philipp" 
>> >> Date: 2015-09-10 16:41:33
>> >> To:  "gromacs.org_gmx-users@maillist.sys.kth.se" <
>> >> gromacs.org_gmx-users@maillist.sys.kth.se>
>> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer
>> >> (martini)
>> >> Hi Kathrin,
>> >> if I remember correctly I once did something similar with g_membed
>> -pieces
>> >> !
>> >>
>> >> Cheers,
>> >> 
>> >> Dr. Jan-Philipp Machtens
>> >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
>> >> Forschungszentrum Jülich, Germany
>> >> Telefon:  02461 616467
>> >> 
>> >>
>> >> 
>> >> Date: Thu, 10 Sep 2015 01:25:00 +0200
>> >> From: Kathrin Hadasch 
>> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer
>> >> (martini)
>> >> Message-ID: <55f0bfcc.7060...@web.de>
>> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>> >>
>> >> Hey you all,
>> >> I'm searching for a way to insert and embed multiple(!) copies of the
>> >> same protein in a complex, presimulated membrane patch (all martini-cg).
>> >> I've tryed lambada for insertion, but I couldn't get it to work with
>> >> more than one protein. I've tried to translate the protein to a (4 4 0)
>> >> vector with editconf in the lambada script, but I get following error:
>> >> Modification of non-creatable array value attempted, subscript -6 at
>> >> /home/lambada/modules/protein.pm line 281.
>> >> For insertion via vmd, I have no clue how to generate a psf file for
>> >> martini-lipids.
>> >> Any suggestions how I could make it work?
>> >> Best regards and thanks in advance,
>> >> Kathrin
>> >>
>> >>
>> >>
>> >>
>> 
>> >>
>> >>
>> 
>> >> Forschungszentrum Juelich GmbH
>> >> 52425 Juelich
>> >> Sitz der Gesellschaft: Juelich
>> >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>> >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>> >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
>> >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>> >> Prof. Dr. Sebastian M. Schmidt
>> >>
>> >>
>> 
>> >>
>> >>
>> 
>> >>

Re: [gmx-users] membrane protein simulation

2015-09-13 Thread Tsjerk Wassenaar 
Hi Brett,

Say I'm designing this new type of truck. Because the earth  it's riding
over is round, do you think I need to adjust the wheel positions on front
and back to match the curvature of the earth?

Cheers,

Tsjerk
On Sep 13, 2015 08:52, "Brett"  wrote:

>
> Dear All,
>
> Suppose a membrane protein contains 10 trans-membrane helix, and as the
> cell membrane is round, the upper and lower part of the 10 trans- membrane
> are not horizontal as they are part of the rounded cell, will you please
> introduce to me how to make the lipid bilayer in curve to parallel the
> upper and lower part of the 10 tran- membrane? I only know we can pack the
> membrane protein into the lipid bilayer in the way the lipid bilayer would
> be perpendicular to the membrane protein.
>
> Yesterday I have posted a similar question but my post was not show in the
> post list.
>
> I am looking forward to getting your reply.
>
>
> Best regards.
>
>
> Brett
>
>
>
>
>
>
>
>
>  Forwarding messages 
> From: "Machtens, Jan-Philipp" 
> Date: 2015-09-10 16:41:33
> To:  "gromacs.org_gmx-users@maillist.sys.kth.se" <
> gromacs.org_gmx-users@maillist.sys.kth.se>
> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer
> (martini)
> Hi Kathrin,
> if I remember correctly I once did something similar with g_membed -pieces
> !
>
> Cheers,
> 
> Dr. Jan-Philipp Machtens
> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
> Forschungszentrum Jülich, Germany
> Telefon:  02461 616467
> 
>
> 
> Date: Thu, 10 Sep 2015 01:25:00 +0200
> From: Kathrin Hadasch 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Multiple membrane proteins in complex bilayer
> (martini)
> Message-ID: <55f0bfcc.7060...@web.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
> Hey you all,
> I'm searching for a way to insert and embed multiple(!) copies of the
> same protein in a complex, presimulated membrane patch (all martini-cg).
> I've tryed lambada for insertion, but I couldn't get it to work with
> more than one protein. I've tried to translate the protein to a (4 4 0)
> vector with editconf in the lambada script, but I get following error:
> Modification of non-creatable array value attempted, subscript -6 at
> /home/lambada/modules/protein.pm line 281.
> For insertion via vmd, I have no clue how to generate a psf file for
> martini-lipids.
> Any suggestions how I could make it work?
> Best regards and thanks in advance,
> Kathrin
>
>
>
> 
>
> 
> Forschungszentrum Juelich GmbH
> 52425 Juelich
> Sitz der Gesellschaft: Juelich
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
>
> 
>
> 
>
> --
> 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.
>
>
>
>
>
>
>
>
>
>
>
>
> --
> 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
>
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> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] membrane protein simulation

2015-09-13 Thread Tsjerk Wassenaar 
Hi Brett,

If you mean an online server, then probably the CHARMM-GUI was made for
you. If you mean downloadable, then you can try inflategro or insane
(coarse-grained). In addition, Gromacs comes with g_membed integrated.

Cheers,

Tsjerk
On Sep 13, 2015 12:00, "Brett"  wrote:

> Dear Tsjerk,
>
> Thanks for the reply. Will you please introduce to me sevral membrane
> builders whith results compatible with gromacs, especially on-line
> available membrane builders?
>
> Best regards.
>
> Brett
>
>
>
>
>
>
>
> At 2015-09-13 17:45:52, "Tsjerk Wassenaar"  wrote:
> >Hi Brett,
> >
> >So apart from the curvature of the membrane, there maybe the situation
> that
> >there's just more of the protein in one leaflet than in the other. You'll
> >need to account for that when embedding. Membrane builders typically check
> >for overlaps to take care of this.
> >
> >Cheers,
> >
> >Tsjerk
> >On Sep 13, 2015 11:37, "Brett"  wrote:
> >
> >> Thanks for the reply Tsjerk. In fact I am just wonding if the situation
> >> exist, i.e., for the  10th trans-membrane helices in the protein, the
> 8th
> >> and or 9th for example is/are a little shorter than the other several
> >> helices. Will you please give a comment on how to process this kind of
> >> membrane protein embeding in lipid  Tsjerk?
> >>
> >> Brett
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> At 2015-09-13 15:19:56, "Tsjerk Wassenaar"  wrote:
> >> >Hi Brett,
> >> >
> >> >Say I'm designing this new type of truck. Because the earth  it's
> riding
> >> >over is round, do you think I need to adjust the wheel positions on
> front
> >> >and back to match the curvature of the earth?
> >> >
> >> >Cheers,
> >> >
> >> >Tsjerk
> >> >On Sep 13, 2015 08:52, "Brett"  wrote:
> >> >
> >> >>
> >> >> Dear All,
> >> >>
> >> >> Suppose a membrane protein contains 10 trans-membrane helix, and as
> the
> >> >> cell membrane is round, the upper and lower part of the 10 trans-
> >> membrane
> >> >> are not horizontal as they are part of the rounded cell, will you
> please
> >> >> introduce to me how to make the lipid bilayer in curve to parallel
> the
> >> >> upper and lower part of the 10 tran- membrane? I only know we can
> pack
> >> the
> >> >> membrane protein into the lipid bilayer in the way the lipid bilayer
> >> would
> >> >> be perpendicular to the membrane protein.
> >> >>
> >> >> Yesterday I have posted a similar question but my post was not show
> in
> >> the
> >> >> post list.
> >> >>
> >> >> I am looking forward to getting your reply.
> >> >>
> >> >>
> >> >> Best regards.
> >> >>
> >> >>
> >> >> Brett
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>  Forwarding messages 
> >> >> From: "Machtens, Jan-Philipp" 
> >> >> Date: 2015-09-10 16:41:33
> >> >> To:  "gromacs.org_gmx-users@maillist.sys.kth.se" <
> >> >> gromacs.org_gmx-users@maillist.sys.kth.se>
> >> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex
> bilayer
> >> >> (martini)
> >> >> Hi Kathrin,
> >> >> if I remember correctly I once did something similar with g_membed
> >> -pieces
> >> >> !
> >> >>
> >> >> Cheers,
> >> >> 
> >> >> Dr. Jan-Philipp Machtens
> >> >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4)
> >> >> Forschungszentrum Jülich, Germany
> >> >> Telefon:  02461 616467
> >> >> 
> >> >>
> >> >> 
> >> >> Date: Thu, 10 Sep 2015 01:25:00 +0200
> >> >> From: Kathrin Hadasch 
> >> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer
> >> >> (martini)
> >> >> Message-ID: <55f0bfcc.7060...@web.de>
> >> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
> >> >>
> >> >> Hey you all,
> >> >> I'm searching for a way to insert and embed multiple(!) copies of the
> >> >> same protein in a complex, presimulated membrane patch (all
> martini-cg).
> >> >> I've tryed lambada for insertion, but I couldn't get it to work with
> >> >> more than one protein. I've tried to translate the protein to a (4 4
> 0)
> >> >> vector with editconf in the lambada script, but I get following
> error:
> >> >> Modification of non-creatable array value attempted, subscript -6 at
> >> >> /home/lambada/modules/protein.pm line 281.
> >> >> For insertion via vmd, I have no clue how to generate a psf file for
> >> >> martini-lipids.
> >> >> Any suggestions how I could make it work?
> >> >> Best regards and thanks in advance,
> >> >> Kathrin
> >> >>
> >> >>
> >> >>
> >> >>
> >>
> 
> >> >>
> >> >>
> >>
> 
> >> >> Forschungszentrum Juelich GmbH
> >> >> 52425 Juelich
>

Re: [gmx-users] membrane protein simulation

2015-04-24 Thread Mostafa Javaheri 
Hi Tsjerk,

Yes, it would be very helpful. thanks for your help.

Best regards,

Mostafa

On Thu, Apr 23, 2015 at 9:40 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Mostafa,

 We have a complete simulation system of bacteriorhodopsin in the purple
 membrane, which you can use as basis for your simulations if you want.

 Best,

 Tsjerk
 On Apr 22, 2015 10:08 PM, Mostafa Javaheri javaheri.grom...@gmail.com
 wrote:

  Dear Justin
  I am going to simulate a homo trimer trans-membrane protein; Base on the
  crystallographic structures there is 7 phosphatidyl glycerol phosphate
  (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or
 3-HSO 3
  -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
  extracellular side of membrane. In the membrane protein tutorial of
 gromacs
  1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced
 as
  the standard lipids, so should I treat PGPs and glycolipids as ligands
 and
  going through protein ligand complex tutorial?
  Or treat glycolipids as ligands, continue the membrane protein tutorial
 and
  use DPPCs instead of PGPs?
  Is it OK if I replace PGP with DPPC from the standpoint of simulation?
  Sincerely
  --
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Re: [gmx-users] membrane protein simulation

2015-04-22 Thread Tsjerk Wassenaar 
Hi Mostafa,

We have a complete simulation system of bacteriorhodopsin in the purple
membrane, which you can use as basis for your simulations if you want.

Best,

Tsjerk
On Apr 22, 2015 10:08 PM, Mostafa Javaheri javaheri.grom...@gmail.com
wrote:

 Dear Justin
 I am going to simulate a homo trimer trans-membrane protein; Base on the
 crystallographic structures there is 7 phosphatidyl glycerol phosphate
 (PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3
 -Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
 extracellular side of membrane. In the membrane protein tutorial of gromacs
 1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced as
 the standard lipids, so should I treat PGPs and glycolipids as ligands and
 going through protein ligand complex tutorial?
 Or treat glycolipids as ligands, continue the membrane protein tutorial and
 use DPPCs instead of PGPs?
 Is it OK if I replace PGP with DPPC from the standpoint of simulation?
 Sincerely
 --
 Gromacs Users mailing list

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

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Re: [gmx-users] membrane protein simulation

2015-04-22 Thread Justin Lemkul 



On 4/22/15 4:07 PM, Mostafa Javaheri wrote:

Dear Justin
I am going to simulate a homo trimer trans-membrane protein; Base on the
crystallographic structures there is 7 phosphatidyl glycerol phosphate
(PGP) per each monomer and also 3 glycolipid molecules (S-TGA-1, or 3-HSO 3
-Galpβ1-6ManpR1-2GlcpR-1-archeol) located inside the trimer on the
extracellular side of membrane. In the membrane protein tutorial of gromacs
1,2-dipalmitoyl-*sn*-glycero-3-phosphatidylcholine (DPPC) is introduced as
the standard lipids, so should I treat PGPs and glycolipids as ligands and
going through protein ligand complex tutorial?
Or treat glycolipids as ligands, continue the membrane protein tutorial and
use DPPCs instead of PGPs?
Is it OK if I replace PGP with DPPC from the standpoint of simulation?


The tutorial is a simple example.  It is absolutely NOT any sort of standard 
lipid or model for what you should do.  It's a demonstration to teach you some 
skills and a manner of thinking about a problem.


Choosing a proper force field is issue #1.  The Berger parameters are OK, but 
there are more recent parameter sets that are vastly better.  Issue #2 is what 
lipid(s) is(are) relevant.  In your case, you've got something very different 
that needs to be modeled accordingly.  You need to simulate what's functionally 
relevant, not what a simple tutorial example provides.


-Justin

--
==

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

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

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

==
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Re: [gmx-users] membrane protein simulation - errors

2014-09-18 Thread Justin Lemkul 



On 9/17/14 6:54 PM, Yunlong Liu wrote:

Hi,


I am trying to use Gromacs 5.0 to run membrane protein simulation. I built my 
membrane protein system with POPC membrane and TIP3P water in VMD. Then I used 
gmx pdb2gmx to build gromacs topology files.


My force field is charmm22* and it contains a lipids.rtp entry. It can 
successfully recognize the POPC molecules in my pdb and the water. But it keeps 
complaining something like this :


Processing chain 7 'L' (5360 atoms, 40 residues)
Warning: Starting residue POPC1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC7 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue POPC8 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further 
warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.

Then I modified the residuestypes.dat to add POPC and TIP3 into the file but it 
still keeps complaining.

I tried to ignore this and run grompp -f minim.mdp -c my.gro .. to generate the 
tpr file but I got an error like this:

---
Program gmx, VERSION 5.0-rc1
Source code file: 
/home/yunlong/Downloads/gromacs-5.0-rc1/src/gromacs/gmxpreprocess/toppush.c, 
line: 2393

Fatal error:
Invalid Atomnr j: 5, b2-nr: 3

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---?


I am wondering whether I can do membrane protein simulation in Gromacs without 
building the system in Gromacs.



It's certainly possible, but I'd start with using an actual release version of 
Gromacs, rather than 5.0-rc1.  Try again with 5.0.1.


-Justin

--
==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
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