-MAria
On Fri, Jul 3, 2009 at 12:27 PM, <[email protected]>
wrote:
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Today's Topics:
1. Re: protein covalently bond to ligand (Tsjerk Wassenaar)
2. waters in ion channels (Samik Bhattacharya)
3. Re: waters in ion channels (Itamar Kass)
4. Re: how to center a MARTINI trajectory so that the lipid
bilayer remains at the center of the box (XAvier Periole)
(maria goranovic)
5. Re: Re: how to center a MARTINI trajectory so that the lipid
bilayer remains at the center of the box (XAvier Periole)
(XAvier Periole)
----------------------------------------------------------------------
Message: 1
Date: Fri, 3 Jul 2009 12:03:48 +0200
From: Tsjerk Wassenaar <[email protected]>
Subject: Re: [gmx-users] protein covalently bond to ligand
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
Hi [email protected],
I think it's better to only use PRODRG for the pyridoxal phosphate
part. Then you can process the rest of the protein as usual,
preserving the parameters for lysine backbone and side chain. The PLP
part you can renumber and merge with the protein topology, adding
bond, angles and dihedrals for the connection. Alternatively you could
rewrite the PLP topology as a .rtp entry and add the connection in the
file specbond.dat.
Hope it helps,
Tsjerk
On Fri, Jul 3, 2009 at 9:03 AM, hazizian<[email protected]>
wrote:
> Hi
> I want to do MD with a protien with prydoxal phosphate(PLP) which
attache
> covalently to one lysine.
> For this I extract the Toplogy of lysine-PLP from PRODRG server.
(DRGGMX.ITP
> and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp.
> after donig
> pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP
> (m.pdb=protein whitout covalent bond) , I modified the topol.top
file
> followig this:
> 1- add "DRG.itp" under the forcefield section on topol.top
> 2- add "DRG 1" under the molecule sectin of topol.top
> also I modifed m1.pdb:
> cut the related lysine (LYS 360) in the m1.pdb and paste the
modified lysine-
> PLP (DRG 360)coordination from DRGPH.PDB.
> then I do editconf -f m1.pdb and genbox -f m1.pdb successfully,
but when I
> want to do grompp the following fatal error appeared:
> There is no DRG moleculetype.
> what should I do now?
> Thanks.
> --
> Tehran University of Medical Sciences
> www.tums.ac.ir
>
>
> --
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> _______________________________________________
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
------------------------------
Message: 2
Date: Fri, 3 Jul 2009 15:38:42 +0530 (IST)
From: Samik Bhattacharya <[email protected]>
Subject: [gmx-users] waters in ion channels
To: Gromacs <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
hi i'm simulating a ion channel protein in DPPC membrane. i'm
following Justin's tutorial for that. and have completed upto the
solvation step. but right after solvation, i found some water
molecules in the channel. now i want to delete those molecules. in
the tutorial it is advised tyo use the keepbyz script to do that..
but after using that i didn't find any change in the structure.
watres are still present in there. may be i am making some mistake
in running the program or something like that!!! can anyone suggest
any thing to solve the problem...thanking you all in advance.
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Message: 3
Date: Fri, 3 Jul 2009 20:12:37 +1000
From: Itamar Kass <[email protected]>
Subject: Re: [gmx-users] waters in ion channels
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[email protected]>
Content-Type: text/plain; charset=ISO-8859-1
Hi,
I would say that those are water molecule which enter from the bulk
water. This is normal and probably important for the physiological
function of the system.
Best,
Itamar
On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya<[email protected]
> wrote:
> hi i'm simulating a ion channel protein in DPPC membrane. i'm
following
> Justin's tutorial for that. and have completed upto the solvation
step. but
> right after solvation, i found some water molecules in the
channel. now i
> want to delete those molecules. in the tutorial it is advised tyo
use the
> keepbyz script to do that.. but after using that i didn't find
any change
> in the structure. watres are still present in there. may be i am
making some
> mistake in running the program or something like that!!! can
anyone suggest
> any thing to solve the problem...thanking you all in advance.
>
> ________________________________
> Yahoo! recommends that you upgrade to the new and safer Internet
Explorer 8.
> _______________________________________________
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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------------------------------
Message: 4
Date: Fri, 3 Jul 2009 12:19:48 +0200
From: maria goranovic <[email protected]>
Subject: [gmx-users] Re: how to center a MARTINI trajectory so that
the lipid bilayer remains at the center of the box
(XAvier Periole)
To: [email protected]
Message-ID:
<[email protected]>
Content-Type: text/plain; charset="iso-8859-1"
Well the bilayer drifts down in the z-direction, and eventually the
leaflets
almost separate, with each leaflet being on opposite ends of the box.
if i try pbc nojump, the lipids drift far away from the box in the
xy plane
On Fri, Jul 3, 2009 at 12:00 PM, <[email protected]>
wrote:
> Send gmx-users mailing list submissions to
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>
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> [email protected]
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> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: how to center a MARTINI trajectory so that the lipid
> bilayer remains at the center of the box (XAvier Periole)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Jul 2009 11:43:55 +0200
> From: XAvier Periole <[email protected]>
> Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
> the lipid bilayer remains at the center of the box
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> What is the problem exactly? The two layers separate over the pbc?
> did you try a -pbc nojump prior the centering?
>
> On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
>
> > Dear All,
> >
> > This has been discussed before for individual frames. But I am
> > having a problem in trying to center a trajectory so that the
> > bilayer remains at the center of the box. I have tried several
> > combinations, but none of the them work. In each case, the
centering
> > and/or the fitting is done on the lipid bilayer itself.
> >
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > center -boxcenter zero -pbc mol
> >
> > this one works for one particular .gro file, but not for the whole
> > trajectory. I tried all of the following, but none of them work.
> > What is the solution ?
> >
> >
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > center -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
pbc
> > mol -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
pbc
> > mol -center
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans -center
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans -center -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
fit
> > trans
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
fit
> > progressive
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> > _______________________________________________
> > gmx-users mailing list [email protected]
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please 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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> End of gmx-users Digest, Vol 63, Issue 11
> *****************************************
>
--
Maria G.
Technical University of Denmark
Copenhagen
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Message: 5
Date: Fri, 3 Jul 2009 12:26:43 +0200
From: XAvier Periole <[email protected]>
Subject: Re: [gmx-users] Re: how to center a MARTINI trajectory so
that the lipid bilayer remains at the center of the
box (XAvier
Periole)
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset="us-ascii"
This sounds pretty bad! You have a drift of your all system
apparently ...
Did you not remove the COM of your system?
For membranes it is often recommended to remove the water and the
lipid bilayer separately. The might drift one from the other.
On Jul 3, 2009, at 12:19 PM, maria goranovic wrote:
> Well the bilayer drifts down in the z-direction, and eventually the
> leaflets almost separate, with each leaflet being on opposite ends
> of the box.
>
> if i try pbc nojump, the lipids drift far away from the box in the
> xy plane
>
> On Fri, Jul 3, 2009 at 12:00 PM, <[email protected]>
> wrote:
> Send gmx-users mailing list submissions to
> [email protected]
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> [email protected]
>
> You can reach the person managing the list at
> [email protected]
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: how to center a MARTINI trajectory so that the lipid
> bilayer remains at the center of the box (XAvier Periole)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 3 Jul 2009 11:43:55 +0200
> From: XAvier Periole <[email protected]>
> Subject: Re: [gmx-users] how to center a MARTINI trajectory so that
> the lipid bilayer remains at the center of the box
> To: Discussion list for GROMACS users <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> What is the problem exactly? The two layers separate over the pbc?
> did you try a -pbc nojump prior the centering?
>
> On Jul 3, 2009, at 11:37 AM, maria goranovic wrote:
>
> > Dear All,
> >
> > This has been discussed before for individual frames. But I am
> > having a problem in trying to center a trajectory so that the
> > bilayer remains at the center of the box. I have tried several
> > combinations, but none of the them work. In each case, the
centering
> > and/or the fitting is done on the lipid bilayer itself.
> >
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > center -boxcenter zero -pbc mol
> >
> > this one works for one particular .gro file, but not for the whole
> > trajectory. I tried all of the following, but none of them work.
> > What is the solution ?
> >
> >
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > center -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
pbc
> > mol -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
pbc
> > mol -center
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans -center
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
> > pbc mol -fit trans -center -boxcenter zero
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
fit
> > trans
> > trjconv -s struct-1.tpr -f temp.xtc -o final.xtc -n struct.ndx -
fit
> > progressive
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> > _______________________________________________
> > gmx-users mailing list [email protected]
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please 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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>
> End of gmx-users Digest, Vol 63, Issue 11
> *****************************************
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> _______________________________________________
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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*****************************************
--
Maria G.
Technical University of Denmark
Copenhagen
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