[gmx-users] Re: Inflategro for Coarse Grained

sunny mishra mishra.sunny at gmail.com
Thu Oct 29 21:05:34 CET 2009 

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?

Sunny

On Thu, Oct 29, 2009 at 1:51 PM, sunny mishra <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>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>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 wrote:
>>> > Send gmx-users mailing list submissions to
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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>
>>> > Subject: [gmx-users] Inflategro for Coarse Grained
>>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> > Message-ID:
>>> >       <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 --------------
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>>> 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>
>>> > Subject: Re: [gmx-users] Inflategro for Coarse Grained
>>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> > Message-ID: <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
>>> > > 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
>>> >
>>> > --
>>> > ========================================
>>> >
>>> > 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
>>> >
>>> > ========================================
>>> >
>>> >
>>> > ------------------------------
>>> >
>>> > Message: 3
>>> > Date: Thu, 29 Oct 2009 09:07:58 +1100
>>> > From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> > Subject: Re: [gmx-users] grompp segfault
>>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> > Message-ID: <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>
>>> > Subject: Re: [gmx-users] em ok, md wrong
>>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> > Message-ID:
>>> >       <3e4d8d8d0910281620o7cef2103nb751716e5541c5b at mail.gmail.com>
>>> > Content-Type: text/plain; charset="iso-8859-1"
>>> >
>>> > 2009/10/28 Liliya Shamova <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 --------------
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>>> >
>>> > ------------------------------
>>> >
>>> > Message: 5
>>> > Date: Wed, 28 Oct 2009 20:19:53 -0400
>>> > From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> > Subject: Re: [gmx-users] em ok, md wrong
>>> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> > Message-ID: <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>>
>>> > >
>>> > >     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
>>> > > 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
>>> >
>>>
>>>
>>
>
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