Sunny
On Thu, Oct 29, 2009 at 1:51 PM, sunny mishra <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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,
[email protected]
<mailto:[email protected]> 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 <[email protected]
<mailto:[email protected]>>
> Subject: [gmx-users] Inflategro for Coarse Grained
> To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> Message-ID:
>
<[email protected]
<mailto:[email protected]>>
> 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" <[email protected]
<mailto:[email protected]>>
> Subject: Re: [gmx-users] Inflategro for Coarse Grained
> To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> Message-ID: <[email protected]
<mailto:[email protected]>>
> 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 [email protected]
<mailto:[email protected]>
> > 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.
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> > Can't post? Read
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>
> --
> ========================================
>
> 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 <[email protected]
<mailto:[email protected]>>
> Subject: Re: [gmx-users] grompp segfault
> To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> Message-ID: <[email protected]
<mailto:[email protected]>>
> 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 <[email protected]
<mailto:[email protected]>>
> Subject: Re: [gmx-users] em ok, md wrong
> To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> Message-ID:
>
<[email protected]
<mailto:[email protected]>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 2009/10/28 Liliya Shamova <[email protected]
<mailto:[email protected]>>
>
> > 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" <[email protected]
<mailto:[email protected]>>
> Subject: Re: [gmx-users] em ok, md wrong
> To: Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> Message-ID: <[email protected]
<mailto:[email protected]>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Yuri Garmay wrote:
> > 2009/10/28 Liliya Shamova <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>>
> >
> > 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 [email protected]
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> > 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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>
------------------------------------------------------------------------
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