[gmx-users] Fwd: Re: Inflategro for Coarse Grained

Thomas Schmidt schmidt at bit.uni-bonn.de
Tue Nov 3 16:27:14 CET 2009 

-------- Forwarded Message --------
From: Thomas Schmidt <schmidt at bit.uni-bonn.de>
Reply-To: schmidt at bit.uni-bonn.de
To: mishra.sunny at gmail.com
Subject: Re: Inflategro for Coarse Grained
Date: Thu, 29 Oct 2009 13:45:02 +0100

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:
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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
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> ------------------------------
> 
> 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
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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
> 
> ========================================
> 
> 
> ------------------------------
> 
> 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?
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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
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>

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