[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!
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>             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
>              > 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
>              >
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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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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