[gmx-users] DOPC lipid bilayer
naga raju
nagaraju_cy at yahoo.co.in
Mon Apr 23 11:07:59 CEST 2007
Dear gmx users,
I am thankful to Tsjerk Wassenaar and Chris Neale, to their suggestions. I prepared dopc.itp parameter file for DOPC lipid bilayer. To Protein+DOPC bilayer system, which force field I have to choose to my protein.
any suggestions is appreciated.
Thanks in advance,
with regards,
Nagaraju Mulpuri.
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Today's Topics:
1. about specbond.dat (Rui Li)
2. Re: about specbond.dat (David van der Spoel)
3. Re: regarding DOPC lipid parameters (Tsjerk Wassenaar)
4. Re: regarding DOPC lipid parameters (Chris Neale)
5. How to get topology file for OPLS (Rui Li)
----------------------------------------------------------------------
Message: 1
Date: Sat, 21 Apr 2007 17:59:47 +0800
From: "Rui Li"
Subject: [gmx-users] about specbond.dat
To: gmx-users at gromacs.org
Message-ID: <377149587.04367 at mail.sdu.edu.cn>
Content-Type: text/plain
Dear all,
In specbond.dat, there are five entries. what meanings they are?
5
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEME FE 2 0.25 CYS2 HEME
CYS SG 1 HEME CAB 1 0.2 CYS2 HEME
CYS SG 1 HEME CAC 1 0.2 CYS2 HEME
HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
I want to add special bond to specbond.dat.How can I do this , can you give me an
example?
Thanks in advance!
------------------------------
Message: 2
Date: Sat, 21 Apr 2007 12:15:07 +0200
From: David van der Spoel
Subject: Re: [gmx-users] about specbond.dat
To: Rui Li , Discussion list for GROMACS
users
Message-ID: <4629E42B.4070009 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Rui Li wrote:
> Dear all,
>
> In specbond.dat, there are five entries. what meanings they are?
> 5
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> CYS SG 1 HEME FE 2 0.25 CYS2 HEME
> CYS SG 1 HEME CAB 1 0.2 CYS2 HEME
> CYS SG 1 HEME CAC 1 0.2 CYS2 HEME
> HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
>
> I want to add special bond to specbond.dat.How can I do this , can you give me an
> example?
the examples are above!
res atom nbonds res atom nbonds bondleng res_newname res_newname
check the archives
>
> Thanks in advance!
>
>
> _______________________________________________
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 3
Date: Sat, 21 Apr 2007 13:40:43 +0200
From: "Tsjerk Wassenaar"
Subject: Re: [gmx-users] regarding DOPC lipid parameters
To: "Discussion list for GROMACS users"
Message-ID:
<8ff898150704210440x6087e4dn80dee29dc2d567f2 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Nagaraju,
You're mail is rather inaccessible in regards the language. Please try
to phrase your question in clear english, which will be of benefit to
you, as it makes it easier for people to read and answer your
question.
I believe you're problem relates to the parameterization of a lipid
which is not yet available. I'm not sure what force field you want to
use, but the best way to tackle this (and the most didactical) is to
draw DPPC and/or POPC and indicate all atom names, numbers, types and
charges, bonds, pairs, angles, dihedrals and improper dihedrals. Then,
draw your DOPC and do the same, taking the same types for
corresponding atoms, bonds, angles, etc. After that, write the
topology, taking one of the available ones as a template.
Best,
Tsjerk
On 4/21/07, naga raju wrote:
> Dear Gromacs Users,
>
> I searched mailing list for DOPC lipid bilayer
> paramters. I found in one of the mailing list "For CHARMM parameters (which
> I believe Feller uses), there is POPC in top_all27_prot_lipid.rtf. For the
> united atom lternative,
> Tieleman's website has popc.itp. In either case, just copy it to a new DOPC
> definition and modify the palmitoyl into another oleoyl"
> I looked into DPPC.itp and POPC.itp files, it very confused (bonds,
> angles and dihedrals) to me to prepare DOPC.itp. Can any body tell how to
> combined these file and getting DOPC parameters.
> any suggestion is appriciated,
> Thanks in advance,
>
> With regards,
>
> Nagaraju Mulpuri.
>
>
> ________________________________
> Ahhh...imagining that irresistible "new car" smell?
> Check out new cars at Yahoo! Autos.
>
>
> _______________________________________________
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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: 4
Date: Sat, 21 Apr 2007 16:44:53 -0400
From: Chris Neale
Subject: [gmx-users] Re: regarding DOPC lipid parameters
To: gmx-users at gromacs.org
Message-ID: <462A77C5.50400 at utoronto.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
First off: do you absolutely need dopc? If so, here is one way to
generate the parameters.
1. Don't use popc.ito from Tieleman's website with a pdb from Feller's
website. Tieleman PDB's and parameter files are based on
(Berger_1997/Egberts_1994/Jorgensen_1988/Chu_1995/Chyu_1996) and those
parameters are different from the Charmm parameters. Also I am sure that
the atom names differ. So you would be best to either: a) Use all charmm
stuff meaning you need to create the parameters in gromacs format (this
is the more difficult option), or b) stick to what is on Tieleman's website.
2. Load one of the popc PDB files into your favourite viewer (I use VMD)
and display only one lipid and then display all of the atom names. Then
go through Tieleman's popc.itp and look at the [atoms] section and write
down the atom number also beside each atom. Now copy this to a piece of
paper (take up the full page) and photocopy it about 5 times.
3. Go through tieleman's popc.itp [bonds] section and mark each bond
down beside the bond on one of the photocopies of your figure
4. Repeat step 3 on a different photocopy for each of [pairs] and
[angles] and [dihedrals].
5. Now that you understand what each parameter is, it should be simple
to go back and create your dopc.itp file. Don't forget to treat the
double bond properly, especially note that it is not treated exactly as
you might expect in the [pairs] section.
6. Next you need a pdb file. This again is not simple. I would
personally recommend using pymol to build one lipid molecule and then
build your membrane from scratch. However, you could also write a script
to simply extend the tails in some already available popc.pdb membrane.
In the second case you will still have problems with the rotamerization
about the double bond. A 1ns equilibration at 310K followed by a high
temperature pulse for 20ps at 510K and then cool to 360K over 100ps
followed by 4ns at 360K and then a couple ns at 310K should get you to a
proper distribution. This basic idea is from Takaoka et al Biophys J V79
2000 3118-3138. I have tried it myself and it works (I used semiiso
p_coupling) but obtaining a stable final state in which the membranes do
not separate absolutely requires either (a) the initial 310K dynamics in
order to get the tails to intercalate or (b) cool over 100ps, which is a
longer cooling period than they used. I haven't found the need to
determine which was the important part.
I realize that this procedure seems long and tedious. But my advice is
that you cut corners here at your own peril.
------------------------------
Message: 5
Date: Sun, 22 Apr 2007 12:04:20 +0800
From: "Rui Li"
Subject: [gmx-users] How to get topology file for OPLS
To: gmx-users at gromacs.org
Message-ID: <377214660.04261 at mail.sdu.edu.cn>
Content-Type: text/plain
Dear all,
I have a ligand moleculer, and I process it on PRODRG, but it only get top file
for GROMOS force field, I want get the atom type for OPLS, How can I do this?
Thanks in advance!
------------------------------
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