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 <[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]>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]>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] wrote: >>> > Send gmx-users mailing list submissions to >>> > [email protected] >>> > >>> > To subscribe or unsubscribe via the World Wide Web, visit >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users >>> > or, via email, send a message with subject or body 'help' to >>> > [email protected] >>> > >>> > You can reach the person managing the list at >>> > [email protected] >>> > >>> > When replying, please edit your Subject line so it is more specific >>> > than "Re: Contents of gmx-users digest..." >>> > >>> > >>> > 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]> >>> > Subject: [gmx-users] Inflategro for Coarse Grained >>> > To: Discussion list for GROMACS users <[email protected]> >>> > Message-ID: >>> > <[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 >>> > -------------- 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" <[email protected]> >>> > Subject: Re: [gmx-users] Inflategro for Coarse Grained >>> > To: Discussion list for GROMACS users <[email protected]> >>> > Message-ID: <[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] >>> > > 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 [email protected]. >>> > > 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 <[email protected]> >>> > Subject: Re: [gmx-users] grompp segfault >>> > To: Discussion list for GROMACS users <[email protected]> >>> > Message-ID: <[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]> >>> > Subject: Re: [gmx-users] em ok, md wrong >>> > To: Discussion list for GROMACS users <[email protected]> >>> > Message-ID: >>> > <[email protected]> >>> > Content-Type: text/plain; charset="iso-8859-1" >>> > >>> > 2009/10/28 Liliya Shamova <[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? >>> > -------------- 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" <[email protected]> >>> > Subject: Re: [gmx-users] em ok, md wrong >>> > To: Discussion list for GROMACS users <[email protected]> >>> > Message-ID: <[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]>> >>> > > >>> > > 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] >>> > > 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 [email protected]. >>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> > >>> >>> >> >
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