[gmx-users] Re: Inflategro for Coarse Grained
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 29 21:09:26 CET 2009
sunny mishra wrote:
> Dear all,
>
> When I cat the protein.gro and lipid.gro file and make it a single
> system file and update its atoms as per the justin's tutorial and then
> run the inflategro script I don't know but for some reason my protein
> moves out from the origin without even doing the Energy Minimization.
> What should I do in this case?
>
If this is happening, then you haven't properly set the location of the protein
within the box using editconf -center (and specifying the same box dimensions as
the lipid bilayer). If you're going along with my tutorial, make sure you
follow all the instructions exactly. I forgot the set the center once, and this
is exactly what happens.
-Justin
> Sunny
>
> On Thu, Oct 29, 2009 at 1:51 PM, sunny mishra <mishra.sunny at gmail.com
> <mailto:mishra.sunny at gmail.com>> wrote:
>
> Dear Thomas,
>
> I have used the new script as well but that doesn't work either and
> gives me the same error. What changes do you think I have to make.
> If you want I can send you my protein.gro file and bilayer.gro file.
> Please let me know about the same if you have any idea about this.
>
> Thanks
>
> Sunny
>
>
> On Thu, Oct 29, 2009 at 12:23 PM, sunny mishra
> <mishra.sunny at gmail.com <mailto:mishra.sunny at gmail.com>> wrote:
>
> Hi Justin,
>
> Yes I have appropriate box vectors defined in my input.gro file
> and I don't know if I have to go ahead and make changes in the
> script or something. I dnt have much idea about this. What
> changes do you suggest me to do?
>
> Sunny
>
>
> On Thu, Oct 29, 2009 at 8:45 AM, Thomas Schmidt
> <schmidt at bit.uni-bonn.de <mailto:schmidt at bit.uni-bonn.de>> wrote:
>
> Dear Sunny,
>
> Justin's right.
>
> The definition of the lipid-representative atom (P) is done
> in line 280
> and 416 in the old version of inflategro.
> There's also a new version available at our website:
> http://www.csb.bit.uni-bonn.de/downloads.html
>
> Nice greetings,
> Thomas
>
> --
> Thomas H. Schmidt, PhD student
> Computational Structural Biology
> Chair of Life Science Informatics, B-IT
> LIMES-Institute, University of Bonn
> Dahlmannstrasse 2, D-53113 Bonn, Germany
>
> Phone: +49-(0)228-2699 323
> Fax: +49-(0)228-2699 341
> http://www.csb.bit.uni-bonn.de
>
>
> On Do, 2009-10-29 at 12:00 +0100,
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org> wrote:
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> > Today's Topics:
> >
> > 1. Inflategro for Coarse Grained (sunny mishra)
> > 2. Re: Inflategro for Coarse Grained (Justin A. Lemkul)
> > 3. Re: grompp segfault (Mark Abraham)
> > 4. Re: em ok, md wrong (Yuri Garmay)
> > 5. Re: em ok, md wrong (Justin A. Lemkul)
> > 6. Polarizable models (Vitaly V. Chaban)
> >
> >
> >
> ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Wed, 28 Oct 2009 16:49:28 -0400
> > From: sunny mishra <mishra.sunny at gmail.com
> <mailto:mishra.sunny at gmail.com>>
> > Subject: [gmx-users] Inflategro for Coarse Grained
> > To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID:
> >
> <2a00bf3a0910281349ta0acd10qe5043302b846a2cd at mail.gmail.com
> <mailto:2a00bf3a0910281349ta0acd10qe5043302b846a2cd at mail.gmail.com>>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi all,
> >
> > After inserting the protein into the lipid bilayer I am
> working on
> > inflategro script and trying to scale the lipid and do
> energy minimization.
> > Since I am doing everything in CG so I dnt know whether
> inflategro is
> > defined for CG or not? Besides that when I run the script
> provided in
> >
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
> , I don't know
> > why I am getting these errors and what is the issue
> behind that.
> >
> > My errors are something like this:
> >
> > Use of uninitialized value $box_x in multiplication (*)
> at ./INFLATEGRO line
> > 259
> > Use of uninitialized value $box_y in multiplication (*)
> at ./INFLATEGRO line
> > 260
> > Scaling lipids....
> > There are 0 lipids...
> > Illegal divison by zero at ./INFLATEGRO line 300
> >
> > I have no idea about this. Please help me out.
> >
> > Thanks,
> >
> > Sunny
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091028/72ff3fc9/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Wed, 28 Oct 2009 17:15:53 -0400
> > From: "Justin A. Lemkul" <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] Inflategro for Coarse Grained
> > To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID: <4AE8B489.1080402 at vt.edu
> <mailto:4AE8B489.1080402 at vt.edu>>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > sunny mishra wrote:
> > > Hi all,
> > >
> > > After inserting the protein into the lipid bilayer I am
> working on
> > > inflategro script and trying to scale the lipid and do
> energy
> > > minimization. Since I am doing everything in CG so I
> dnt know whether
> > > inflategro is defined for CG or not? Besides that when
> I run the script
> > > provided
> > > in
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis , I
> > > don't know why I am getting these errors and what is
> the issue behind that.
> > >
> > > My errors are something like this:
> > >
> > > Use of uninitialized value $box_x in multiplication (*)
> at ./INFLATEGRO
> > > line 259
> > > Use of uninitialized value $box_y in multiplication (*)
> at ./INFLATEGRO
> > > line 260
> > > Scaling lipids....
> > > There are 0 lipids...
> > > Illegal divison by zero at ./INFLATEGRO line 300
> > >
> > > I have no idea about this. Please help me out.
> > >
> >
> > InflateGRO is hard-coded to search for "P" atoms, common
> to phospholipids. You
> > might have to change the pattern matching specification
> to detect some (unique)
> > atom in your lipid.
> >
> > It also looks like there is a problem with the box
> definition. Do you have
> > appropriate box vectors defined in your input .gro file?
> >
> > -Justin
> >
> > > Thanks,
> > >
> > > Sunny
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > 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
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> <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
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Thu, 29 Oct 2009 09:07:58 +1100
> > From: Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> > Subject: Re: [gmx-users] grompp segfault
> > To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID: <4AE8C0BE.8040801 at anu.edu.au
> <mailto:4AE8C0BE.8040801 at anu.edu.au>>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Birger Dittrich wrote:
> > > Dear Gromacs users,
> > >
> > > I have compiled gromacs 4.0.5 on a suse 10.3 x86-64 box
> > > after having compiled and installed fftw-3.2.2 and
> encountered
> > > no problems.
> > > Now I would like to check whether the installation has
> > > worked ok.
> > > I downloaded the gmxtest test suite, unpacked it in the
> gromacs directory
> > > and tried to run it after sourcing GMXRC. However, the
> test suite fails.
> >
> > Don't bother - it's barely a useful test for GROMACS 4. I
> did some work
> > improving it a few months back
> >
> (http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html),
> > which is in the git version, but apparently there were
> too many
> > outstanding issues for anybody else to be interested in
> working towards
> > releasing a version that did work reliably for GROMACS 4.
> It's
> > unfortunate that there is all this documentation
> suggesting using it and
> > it doesn't work. :-(
> >
> > > The output I get is
> > > (~/gromacs-4.0.5): grompp -h
> > > :-) G R O M A C S (-:
> > >
> > > Segmentation fault
> > >
> > > Has anybody got a clue what I can try to
> > > do to get the grompp running or how I can get more
> information
> > > on the possible cause for the segfault?
> >
> > This failure is not related to the test suite, of course.
> I'd guess you
> > have some problem with dynamic linking of libraries -
> they were present
> > in relevant library paths when you configured, and are
> not now.
> >
> > Mark
> >
> >
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 29 Oct 2009 02:20:50 +0300
> > From: Yuri Garmay <yuri.from.spb at gmail.com
> <mailto:yuri.from.spb at gmail.com>>
> > Subject: Re: [gmx-users] em ok, md wrong
> > To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID:
> >
> <3e4d8d8d0910281620o7cef2103nb751716e5541c5b at mail.gmail.com
> <mailto:3e4d8d8d0910281620o7cef2103nb751716e5541c5b at mail.gmail.com>>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > 2009/10/28 Liliya Shamova <lshamova at yahoo.com
> <mailto:lshamova at yahoo.com>>
> >
> > > Hi everybody!
> > >
> >
> > Dihedrals seem be incorrect. Check it. (I don't know what
> have to be, is it
> > planar molecule or not, it have be known, but it seems to
> be incorrect, as
> > you say molecule distorted) Additionally, you should use
> improper dihedrals
> > for making planar parts.
> >
> > P.S.
> >
> > 1) I think, this acid is charged in neutral pH. OOC-COO
> (2-), not HOOC-COOH
> >
> > 2) Why not to use topology of charged ASP residue side
> chaas starting point?
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091029/ad96994f/attachment-0001.html
> >
> > ------------------------------
> >
> > Message: 5
> > Date: Wed, 28 Oct 2009 20:19:53 -0400
> > From: "Justin A. Lemkul" <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] em ok, md wrong
> > To: Discussion list for GROMACS users
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > Message-ID: <4AE8DFA9.4000904 at vt.edu
> <mailto:4AE8DFA9.4000904 at vt.edu>>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> >
> > Yuri Garmay wrote:
> > > 2009/10/28 Liliya Shamova <lshamova at yahoo.com
> <mailto:lshamova at yahoo.com> <mailto:lshamova at yahoo.com
> <mailto:lshamova at yahoo.com>>>
> > >
> > > Hi everybody!
> > >
> > >
> > > Dihedrals seem be incorrect. Check it. (I don't know
> what have to be, is
> > > it planar molecule or not, it have be known, but it
> seems to be
> > > incorrect, as you say molecule distorted) Additionally,
> you should use
> > > improper dihedrals for making planar parts.
> > >
> >
> > Indeed, the dihedrals don't make much sense. Based on
> ASPH, you should define a
> > HO-OH-C-O dihedral for each carboxylic acid group, and I
> would think you would
> > also need to define an O-C-C-O torsion. All of this
> information is in the
> > ffoplsaabon.itp and ffoplsaa.rtp files. You should
> definitely define impropers
> > to keep the carboxylic acid groups planar. Using the
> ASPH entry in ffoplsaa.rtp
> > is a good start. If hydrogens are collapsing into
> neighboring acid groups, your
> > [pairs] directive is probably incorrect.
> >
> > > P.S.
> > >
> > > 1) I think, this acid is charged in neutral pH. OOC-COO
> (2-), not HOOC-COOH
> >
> > True, but this is (as described) a vacuum simulation, so
> we're not dealing with
> > solution pH.
> >
> > -Justin
> >
> > >
> > > 2) Why not to use topology of charged ASP residue side
> chaas starting point?
> > >
> > >
> > >
> ------------------------------------------------------------------------
> > >
> > > _______________________________________________
> > > 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
> >
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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