[gmx-users] Phosphorylation of protein
rituraj purohit
riturajpurohit at gmail.com
Wed May 19 16:16:34 CEST 2010
Dear friends,
I want to add a phosphate (PO4) group to a amino acid residue (serine)
in my protein molecule (phosphorylation of protein).
Is is possible to do by in-silico (with help of Gromcs or by any other server)?
Please help me in this.
Thank you :)
Rohan
On Wed, May 19, 2010 at 7:32 PM, <gmx-users-request at gromacs.org> wrote:
>
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> 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
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
> gmx-users-owner at gromacs.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: enegry minimisation (Justin A. Lemkul)
> 2. g_cluster, RMSD distribution (Micha? Koli?ski)
> 3. Re: enegry minimisation (Gaurav Goel)
> 4. Re: Re: crystallographic water to tip4p model (????? ?????????)
> 5. Re: enegry minimisation (sonali dhindwal)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 May 2010 09:18:08 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] enegry minimisation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4BF3E510.3040503 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> Gaurav Goel wrote:
> > After adding water you can do energy minimization (EM) in two steps:
> >
> > 1. Constrain the protein backbone and do EM.
> > 2. Now do EM on the full system.
> > 3. Run a short MD simulation by constraining the protein backbone.
> > The above three steps will help hydrate the protein molecule with
> > minimal distortion of protein structure.
> >
>
> Such finesse may certainly be beneficial. Just for clarity, though, what you
> are referring to is the application of (position) restraints, not constraints.
>
> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>
> -Justin
>
> > 4. Now run a MD on full system.
> >
> > for details looks here:
> > http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ
> > <http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ>
> >
> > -Gaurav
> >
> > On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
> > <sonali11dhindwal at yahoo.co.in <mailto:sonali11dhindwal at yahoo.co.in>> wrote:
> >
> > Sorry, but I couldnt get your question,
> > I have used this .mdp file for energy minimisation after addition of
> > water and using
> >
> > GROMOS96 43a1 force field :
> >
> >
> > title = drg_trp
> > cpp = /lib/cpp ; location of cpp on SGI
> > define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
> > constraints = none
> > integrator = steep
> > dt = 0.002 ; ps !
> > nsteps = 2000
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME ; Use particle-mesh ewald
> > rcoulomb = 0.9
> > rvdw = 1.0
> > fourierspacing = 0.12
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > pme_order = 4
> > ewald_rtol = 1e-5
> > optimize_fft = yes
> > ;
> > ; Energy minimizing stuff
> > ;
> > emtol = 1000.0
> > emstep = 0.01
> >
> > I hope it will help you to guide me further
> > Thanks
> > --
> > Sonali Dhindwal
> >
> >
> > --- On *Wed, 19/5/10, Erik Marklund /<erikm at xray.bmc.uu.se
> > <mailto:erikm at xray.bmc.uu.se>>/* wrote:
> >
> >
> > From: Erik Marklund <erikm at xray.bmc.uu.se
> > <mailto:erikm at xray.bmc.uu.se>>
> > Subject: Re: [gmx-users] enegry minimisation
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>>
> > Date: Wednesday, 19 May, 2010, 5:31 PM
> >
> >
> > sonali dhindwal skrev:
> > > Hello All
> > > This question may sound trivial to many, but as i am new to
> > this field, please help.
> > > I want to ask a question regarding my previous query of
> > distortion of protein strucutre after molecular dynamcs simulation.
> > > I have noticed that after enegry minimisation using steepest
> > decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large
> > amount of distortion occurs.
> > > So is it necessary to do enegry minimisation step before MD,
> > because this is my modeled protein, and i have already done
> > energy minimisation using different program and after that I
> > have done refinement also.
> > > Thanks and regards
> > > ^
> > >
> > >
> > > --
> > > Sonali Dhindwal
> > >
> > >
> > So how has your system setup changed since your previous EM?
> > Addition of water? Cutoffs? PME?
> >
> > -- -----------------------------------------------
> > Erik Marklund, PhD student
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: +46 18 471 4537 fax: +46 18 511 755
> > erikm at xray.bmc.uu.se
> > <http://mc/compose?to=erikm@xray.bmc.uu.se>
> > http://folding.bmc.uu.se/
> >
> > -- gmx-users mailing list gmx-users at gromacs.org
> > <http://mc/compose?to=gmx-users@gromacs.org>
> > 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 gmx-users-request at gromacs.org
> > <http://mc/compose?to=gmx-users-request@gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > 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 gmx-users-request at gromacs.org
> > <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 19 May 2010 15:14:50 +0200
> From: Micha? Koli?ski <mkolin at iimcb.gov.pl>
> Subject: [gmx-users] g_cluster, RMSD distribution
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Message-ID:
> <7D0446725B1683488608097329D0FFB90137DAECDFB7 at kolab.iimcb.gov.pl>
> Content-Type: text/plain; charset="windows-1250"
>
> Dear All
>
> I’m trying to obtain RMSD distribution of a ligand in the binding site of the receptor protein during 40 ns MD simulation.
> Could you please explain:
>
> - what is exactly the yaxis unit of the plot obtained using g_cluster with –dist option
> - how is this distribution calculated?
>
> Thank you in advance,
>
> All best,
> Michal
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 19 May 2010 09:29:33 -0400
> From: Gaurav Goel <gauravgoeluta at gmail.com>
> Subject: Re: [gmx-users] enegry minimisation
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTikGPAKyh20mMpG40Xv6fH6WciiRevLeh037gY0x at mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> On Wed, May 19, 2010 at 9:18 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > Gaurav Goel wrote:
> >>
> >> After adding water you can do energy minimization (EM) in two steps:
> >>
> >> 1. Constrain the protein backbone and do EM.
> >> 2. Now do EM on the full system.
> >> 3. Run a short MD simulation by constraining the protein backbone.
> >> The above three steps will help hydrate the protein molecule with minimal
> >> distortion of protein structure.
> >>
> >
> > Such finesse may certainly be beneficial. Just for clarity, though, what
> > you are referring to is the application of (position) restraints, not
> > constraints.
> >
> > http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
> >
> Justin, thanks for clarifying. I was referring to position restraints.
> -Gaurav
> > -Justin
> >
> >> 4. Now run a MD on full system.
> >>
> >> for details looks here:
> >>
> >> http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ
> >> <http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CBcQFjAB&url=http%3A%2F%2Feugen.leitl.org%2Fchem%2Fkerrigje%2Fpdf_files%2Ffwspidr_tutor.pdf&ei=jOPzS8a3Lab2MdX1_aAO&usg=AFQjCNGB_3mXSQRHuqehBSHXsRyXP1Gymg&sig2=bY3NqXHmruR7eSLVyAuCHQ>
> >>
> >> -Gaurav
> >>
> >> On Wed, May 19, 2010 at 8:18 AM, sonali dhindwal
> >> <sonali11dhindwal at yahoo.co.in <mailto:sonali11dhindwal at yahoo.co.in>> wrote:
> >>
> >> Sorry, but I couldnt get your question,
> >> I have used this .mdp file for energy minimisation after addition of
> >> water and using
> >>
> >> GROMOS96 43a1 force field :
> >>
> >>
> >> title = drg_trp
> >> cpp = /lib/cpp ; location of cpp on SGI
> >> define = -DFLEX_SPC ; Use Ferguson’s Flexible water model [4]
> >> constraints = none
> >> integrator = steep
> >> dt = 0.002 ; ps !
> >> nsteps = 2000
> >> nstlist = 10
> >> ns_type = grid
> >> rlist = 0.9
> >> coulombtype = PME ; Use particle-mesh ewald
> >> rcoulomb = 0.9
> >> rvdw = 1.0
> >> fourierspacing = 0.12
> >> fourier_nx = 0
> >> fourier_ny = 0
> >> fourier_nz = 0
> >> pme_order = 4
> >> ewald_rtol = 1e-5
> >> optimize_fft = yes
> >> ;
> >> ; Energy minimizing stuff
> >> ;
> >> emtol = 1000.0
> >> emstep = 0.01
> >>
> >> I hope it will help you to guide me further
> >> Thanks
> >> --
> >> Sonali Dhindwal
> >>
> >>
> >> --- On *Wed, 19/5/10, Erik Marklund /<erikm at xray.bmc.uu.se
> >> <mailto:erikm at xray.bmc.uu.se>>/* wrote:
> >>
> >>
> >> From: Erik Marklund <erikm at xray.bmc.uu.se
> >> <mailto:erikm at xray.bmc.uu.se>>
> >> Subject: Re: [gmx-users] enegry minimisation
> >> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
> >> <mailto:gmx-users at gromacs.org>>
> >> Date: Wednesday, 19 May, 2010, 5:31 PM
> >>
> >>
> >> sonali dhindwal skrev:
> >> > Hello All
> >> > This question may sound trivial to many, but as i am new to
> >> this field, please help.
> >> > I want to ask a question regarding my previous query of
> >> distortion of protein strucutre after molecular dynamcs simulation.
> >> > I have noticed that after enegry minimisation using steepest
> >> decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 , large
> >> amount of distortion occurs.
> >> > So is it necessary to do enegry minimisation step before MD,
> >> because this is my modeled protein, and i have already done
> >> energy minimisation using different program and after that I
> >> have done refinement also.
> >> > Thanks and regards
> >> > ^
> >> >
> >> >
> >> > --
> >> > Sonali Dhindwal
> >> >
> >> >
> >> So how has your system setup changed since your previous EM?
> >> Addition of water? Cutoffs? PME?
> >>
> >> -- -----------------------------------------------
> >> Erik Marklund, PhD student
> >> Dept. of Cell and Molecular Biology, Uppsala University.
> >> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> >> phone: +46 18 471 4537 fax: +46 18 511 755
> >> erikm at xray.bmc.uu.se
> >> <http://mc/compose?to=erikm@xray.bmc.uu.se>
> >> http://folding.bmc.uu.se/
> >>
> >> -- gmx-users mailing list gmx-users at gromacs.org
> >> <http://mc/compose?to=gmx-users@gromacs.org>
> >> 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 gmx-users-request at gromacs.org
> >> <http://mc/compose?to=gmx-users-request@gromacs.org>.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> >> <mailto:gmx-users at gromacs.org>
> >> 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 gmx-users-request at gromacs.org
> >> <mailto:gmx-users-request at gromacs.org>.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >
> > --
> > ========================================
> >
> > 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
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 19 May 2010 17:35:46 +0400
> From: ????? ????????? <pavkudr at gmail.com>
> Subject: [gmx-users] Re: Re: crystallographic water to tip4p model
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTilnxrgPKJ58z2tS4dydTnkmSbovo6LV8r1mXL2T at mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> >> Hi,
> >> I wanna keep crystallographic water with tip4p model for md simulation
> but when I use pdb2gmx even if I set "-water tip4p" it protonates oxygens to
> spc water model instead.
> >> Is there any way to replace spc water molecules with tip4p water
> molecules in the same orientation?
> >
> >What's your GROMACS version and command line?
> >
> >> Btw what happen if I'll keep 2 types of water models in one simulation?
> >
> >Your reviewers will giggle.
> >
> >Mark
>
> Hi
> I’m using following lines to prepare structure
>
> pdb2gmx -f 1KEH.pdb -o 1keh.gro -p 1keh.top -ff oplsaa -water tip4p
> editconf -f 1keh.gro -d 1 -c -bt cubic -o 1keh.box.gro
> genbox -cp 1keh.box.gro -cs tip4p.gro -o 1keh.sol.gro -p 1keh.top
>
> after this in 1keh.sol.gro there are 2 types of water like
> 1078HO4 HW112050 5.331 6.748 7.575
> 1078HO4 HW212051 5.413 6.666 7.459
> 1078HO4 HW312052 5.413 6.748 7.517
> 1079HO4 OW12053 7.630 6.590 7.095
> 1079HO4 HW112054 7.630 6.671 7.037
> 1079HO4 HW212055 7.630 6.508 7.037
> 1079HO4 HW312056 7.630 6.590 7.095
> 1080HO4 OW12057 3.861 4.563 2.433
>
> and like
> 1083SOL OW12069 1.736 0.839 0.257
> 1083SOL HW112070 1.777 0.781 0.322
> 1083SOL HW212071 1.643 0.831 0.274
> 1083SOL MW12072 1.730 0.831 0.267
> 1084SOL OW12073 1.602 0.771 1.252
> 1084SOL HW112074 1.557 0.838 1.303
> 1084SOL HW212075 1.690 0.807 1.238
> 1084SOL MW12076 1.608 0.784 1.256
> as I can understand pdb2gmx converted crystallographic O into H2O with
> additional H in the same place as O instead of additional M near O
> how can it be fixed?
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100519/21438e3d/attachment-0001.html
>
> ------------------------------
>
> Message: 5
> Date: Wed, 19 May 2010 19:31:30 +0530 (IST)
> From: sonali dhindwal <sonali11dhindwal at yahoo.co.in>
> Subject: Re: [gmx-users] enegry minimisation
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID: <930211.32980.qm at web94606.mail.in2.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks Justin for your help
> I checked the mdout.mpd, all the parameters were interpereted correctly, though from next time i will take care of putting space.
> regarding you asked if those are small molecules, yes those are the ligands and i have taken .itp and .gro file from Dundee Prodrg server. I think those are acceptable !!
> Thermostat setup:
> I will now do this thing seperately as protein and non protein only as given in manual.
>
> And also I will do that thing suggested by Gaurav, hopefully it will help in not distorting the protein structure.
> Thanks a lot.
>
> --
> Sonali Dhindwal
>
> --- On Wed, 19/5/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] enegry minimisation
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Wednesday, 19 May, 2010, 5:45 PM
>
>
>
> sonali dhindwal wrote:
> > Thanks Justin for your reply.
> > Yes I have included solvent in the protein using genbox.
>
> Then you should do energy minimization after constructing the system.
>
> > I am pasting .mdp file which I used for MD simulation :
> >
> > title = trp_drg MD
> > cpp = /lib/cpp ; location of cpp on SGI
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 500000 ; total 1 ns.
> > nstcomm =1
>
> I don't know if this matters or not, but I think your parameters and values
> should be separated from the '=' by whitespace. I also don't know if that will have any effect on your unstable system (see below), but do check to make sure that all of your settings have been interpreted correctly. Confirm your input settings with the mdout.mdp file produced by grompp.
>
> > nstxout = 500 ; output coordinates every 1.0 ps
> > nstvout =0
> > nstfout =0
> > nstlist = 5
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw
> = 1.4
> > fourierspacing = 0.12
> > fourier_nx =0
> > fourier_ny =0
> > fourier_nz =0
> > pme_order =6
> > ewald_rtol = 1e-5
> > optimize_fft = yes
> > ; Berendsen temperature coupling is on in four groups
> > Tcoupl = berendsen
> > tau_t = 0.1 0.1 0.1 0.1 0.1 0.1
> > tc_grps = Protein SOL MG PEP E4P NA+
> > ref_t =
> 300 300 300 300 300 300
>
> This thermostat setup is certainly incorrect. You should not couple all the components of your system to separate thermostats. See here:
>
> http://www.gromacs.org/Documentation/Terminology/Thermostats
>
> You have a fairly complicated system. Are some of these species small molecules? If so, how did you derive their parameters? Have you demonstrated that these parameters are accurate? Which structure is falling apart, and how are you making that assessment?
>
> -Justin
>
> > ; Pressure coupling is on
> > Pcoupl = berendsen
> > pcoupltype = isotropic
> > tau_p
> = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
> > I hope it will help you to guide me futher.
> > Thanks
> >
> > --
> > Sonali Dhindwal
> >
> >
> > --- On *Wed, 19/5/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
> >
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] enegry minimisation
> > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> > Date: Wednesday, 19 May, 2010, 5:17 PM
> >
> >
> >
> > sonali dhindwal wrote:
> > > Hello All
> > > This question may sound trivial to many, but as i am new to this
> > field, please help.
> > > I want to ask a question regarding my previous query of
> > distortion of protein strucutre after molecular dynamcs simulation.
> >
> > Can you provide a link to your previous post, for reference?
> >
> > > I have noticed that after enegry minimisation using steepest
> > decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
> >
> > So is it necessary to do enegry minimisation step before MD,
> > because this is my modeled protein, and i have already done energy
> > minimisation using different program and after that I have done
> > refinement also.
> >
> > Have you added solvent or anything else to the protein model? If
> > so, then the answer is yes. Solvation with a regularly-ordered
> > lattice of solvent molecules can (and often does) lead to bad
> > clashes with your protein structure, thus necessitating further
> > minimization.
> >
> > There are plenty of reasons why a protein structure might be
> > unstable, most of them related to .mdp file settings, but
> you
> > haven't posted those so there's no way to know if you're doing
> > things correctly.
> >
> > -Justin
> >
> > > Thanks and regards
> > > ^
> > >
> > > --
> > > Sonali Dhindwal
> > >
> > >
> >
> > -- ========================================
> >
> > 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
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org
> > </mc/compose?to=gmx-users at gromacs.org>
> > 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 gmx-users-request at gromacs.org
> > </mc/compose?to=gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
>
> -- ========================================
>
> 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
>
> ========================================
> -- gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100519/8ee02834/attachment.html
>
> ------------------------------
>
> --
> gmx-users mailing list
> gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 73, Issue 119
> ******************************************
More information about the gromacs.org_gmx-users
mailing list