-------- Forwarded Message -------- From: Thomas Schmidt <schm...@bit.uni-bonn.de> Reply-To: schm...@bit.uni-bonn.de To: mishra.su...@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-requ...@gromacs.org wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > 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 > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > 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 <mishra.su...@gmail.com> > Subject: [gmx-users] Inflategro for Coarse Grained > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <2a00bf3a0910281349ta0acd10qe5043302b846a...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] Inflategro for Coarse Grained > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4ae8b489.1080...@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@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-requ...@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.abra...@anu.edu.au> > Subject: Re: [gmx-users] grompp segfault > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4ae8c0be.8040...@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....@gmail.com> > Subject: Re: [gmx-users] em ok, md wrong > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <3e4d8d8d0910281620o7cef2103nb751716e5541...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 2009/10/28 Liliya Shamova <lsham...@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" <jalem...@vt.edu> > Subject: Re: [gmx-users] em ok, md wrong > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4ae8dfa9.4000...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Yuri Garmay wrote: > > 2009/10/28 Liliya Shamova <lsham...@yahoo.com <mailto:lsham...@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@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
