Dear all,<div><br></div><div>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?</div>
<div><br></div><div>Sunny<br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 1:51 PM, sunny mishra <span dir="ltr"><<a href="mailto:mishra.sunny@gmail.com">mishra.sunny@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear Thomas,<div><br></div><div>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.</div>
<div><br></div><div>Thanks</div><div><br></div><div><font color="#888888">Sunny</font><div><div></div><div class="h5"><br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 12:23 PM, sunny mishra <span dir="ltr"><<a href="mailto:mishra.sunny@gmail.com" target="_blank">mishra.sunny@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Justin,<br><br>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?<br>
<font color="#888888">
<br>Sunny</font><div><div></div><div><br><br><div class="gmail_quote">On Thu, Oct 29, 2009 at 8:45 AM, Thomas Schmidt <span dir="ltr"><<a href="mailto:schmidt@bit.uni-bonn.de" target="_blank">schmidt@bit.uni-bonn.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left:1px solid rgb(204, 204, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex">
Dear Sunny,<br>
<br>
Justin's right.<br>
<br>
The definition of the lipid-representative atom (P) is done in line 280<br>
and 416 in the old version of inflategro.<br>
There's also a new version available at our website:<br>
<a href="http://www.csb.bit.uni-bonn.de/downloads.html" target="_blank">http://www.csb.bit.uni-bonn.de/downloads.html</a><br>
<br>
Nice greetings,<br>
Thomas<br>
<br>
--<br>
Thomas H. Schmidt, PhD student<br>
Computational Structural Biology<br>
Chair of Life Science Informatics, B-IT<br>
LIMES-Institute, University of Bonn<br>
Dahlmannstrasse 2, D-53113 Bonn, Germany<br>
<br>
Phone: +49-(0)228-2699 323<br>
Fax: +49-(0)228-2699 341<br>
<a href="http://www.csb.bit.uni-bonn.de" target="_blank">http://www.csb.bit.uni-bonn.de</a><br>
<br>
<br>
On Do, 2009-10-29 at 12:00 +0100, <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a> wrote:<br>
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> Today's Topics:<br>
><br>
> 1. Inflategro for Coarse Grained (sunny mishra)<br>
> 2. Re: Inflategro for Coarse Grained (Justin A. Lemkul)<br>
> 3. Re: grompp segfault (Mark Abraham)<br>
> 4. Re: em ok, md wrong (Yuri Garmay)<br>
> 5. Re: em ok, md wrong (Justin A. Lemkul)<br>
> 6. Polarizable models (Vitaly V. Chaban)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Wed, 28 Oct 2009 16:49:28 -0400<br>
> From: sunny mishra <<a href="mailto:mishra.sunny@gmail.com" target="_blank">mishra.sunny@gmail.com</a>><br>
> Subject: [gmx-users] Inflategro for Coarse Grained<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> Message-ID:<br>
> <<a href="mailto:2a00bf3a0910281349ta0acd10qe5043302b846a2cd@mail.gmail.com" target="_blank">2a00bf3a0910281349ta0acd10qe5043302b846a2cd@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Hi all,<br>
><br>
> After inserting the protein into the lipid bilayer I am working on<br>
> inflategro script and trying to scale the lipid and do energy minimization.<br>
> Since I am doing everything in CG so I dnt know whether inflategro is<br>
> defined for CG or not? Besides that when I run the script provided in<br>
> <a href="http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis</a> , I don't know<br>
> why I am getting these errors and what is the issue behind that.<br>
><br>
> My errors are something like this:<br>
><br>
> Use of uninitialized value $box_x in multiplication (*) at ./INFLATEGRO line<br>
> 259<br>
> Use of uninitialized value $box_y in multiplication (*) at ./INFLATEGRO line<br>
> 260<br>
> Scaling lipids....<br>
> There are 0 lipids...<br>
> Illegal divison by zero at ./INFLATEGRO line 300<br>
><br>
> I have no idea about this. Please help me out.<br>
><br>
> Thanks,<br>
><br>
> Sunny<br>
> -------------- next part --------------<br>
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><br>
> ------------------------------<br>
><br>
> Message: 2<br>
> Date: Wed, 28 Oct 2009 17:15:53 -0400<br>
> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
> Subject: Re: [gmx-users] Inflategro for Coarse Grained<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4AE8B489.1080402@vt.edu" target="_blank">4AE8B489.1080402@vt.edu</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
><br>
><br>
> sunny mishra wrote:<br>
> > Hi all,<br>
> ><br>
> > After inserting the protein into the lipid bilayer I am working on<br>
> > inflategro script and trying to scale the lipid and do energy<br>
> > minimization. Since I am doing everything in CG so I dnt know whether<br>
> > inflategro is defined for CG or not? Besides that when I run the script<br>
> > provided<br>
> > in <a href="http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis</a> , I<br>
> > don't know why I am getting these errors and what is the issue behind that.<br>
> ><br>
> > My errors are something like this:<br>
> ><br>
> > Use of uninitialized value $box_x in multiplication (*) at ./INFLATEGRO<br>
> > line 259<br>
> > Use of uninitialized value $box_y in multiplication (*) at ./INFLATEGRO<br>
> > line 260<br>
> > Scaling lipids....<br>
> > There are 0 lipids...<br>
> > Illegal divison by zero at ./INFLATEGRO line 300<br>
> ><br>
> > I have no idea about this. Please help me out.<br>
> ><br>
><br>
> InflateGRO is hard-coded to search for "P" atoms, common to phospholipids. You<br>
> might have to change the pattern matching specification to detect some (unique)<br>
> atom in your lipid.<br>
><br>
> It also looks like there is a problem with the box definition. Do you have<br>
> appropriate box vectors defined in your input .gro file?<br>
><br>
> -Justin<br>
><br>
> > Thanks,<br>
> ><br>
> > Sunny<br>
> ><br>
> ><br>
> > ------------------------------------------------------------------------<br>
> ><br>
> > _______________________________________________<br>
> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> > Please don't post (un)subscribe requests to the list. Use the<br>
> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 3<br>
> Date: Thu, 29 Oct 2009 09:07:58 +1100<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
> Subject: Re: [gmx-users] grompp segfault<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4AE8C0BE.8040801@anu.edu.au" target="_blank">4AE8C0BE.8040801@anu.edu.au</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
> Birger Dittrich wrote:<br>
> > Dear Gromacs users,<br>
> ><br>
> > I have compiled gromacs 4.0.5 on a suse 10.3 x86-64 box<br>
> > after having compiled and installed fftw-3.2.2 and encountered<br>
> > no problems.<br>
> > Now I would like to check whether the installation has<br>
> > worked ok.<br>
> > I downloaded the gmxtest test suite, unpacked it in the gromacs directory<br>
> > and tried to run it after sourcing GMXRC. However, the test suite fails.<br>
><br>
> Don't bother - it's barely a useful test for GROMACS 4. I did some work<br>
> improving it a few months back<br>
> (<a href="http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html</a>),<br>
> which is in the git version, but apparently there were too many<br>
> outstanding issues for anybody else to be interested in working towards<br>
> releasing a version that did work reliably for GROMACS 4. It's<br>
> unfortunate that there is all this documentation suggesting using it and<br>
> it doesn't work. :-(<br>
><br>
> > The output I get is<br>
> > (~/gromacs-4.0.5): grompp -h<br>
> > :-) G R O M A C S (-:<br>
> ><br>
> > Segmentation fault<br>
> ><br>
> > Has anybody got a clue what I can try to<br>
> > do to get the grompp running or how I can get more information<br>
> > on the possible cause for the segfault?<br>
><br>
> This failure is not related to the test suite, of course. I'd guess you<br>
> have some problem with dynamic linking of libraries - they were present<br>
> in relevant library paths when you configured, and are not now.<br>
><br>
> Mark<br>
><br>
><br>
> ------------------------------<br>
><br>
> Message: 4<br>
> Date: Thu, 29 Oct 2009 02:20:50 +0300<br>
> From: Yuri Garmay <<a href="mailto:yuri.from.spb@gmail.com" target="_blank">yuri.from.spb@gmail.com</a>><br>
> Subject: Re: [gmx-users] em ok, md wrong<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> Message-ID:<br>
> <<a href="mailto:3e4d8d8d0910281620o7cef2103nb751716e5541c5b@mail.gmail.com" target="_blank">3e4d8d8d0910281620o7cef2103nb751716e5541c5b@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> 2009/10/28 Liliya Shamova <<a href="mailto:lshamova@yahoo.com" target="_blank">lshamova@yahoo.com</a>><br>
><br>
> > Hi everybody!<br>
> ><br>
><br>
> Dihedrals seem be incorrect. Check it. (I don't know what have to be, is it<br>
> planar molecule or not, it have be known, but it seems to be incorrect, as<br>
> you say molecule distorted) Additionally, you should use improper dihedrals<br>
> for making planar parts.<br>
><br>
> P.S.<br>
><br>
> 1) I think, this acid is charged in neutral pH. OOC-COO (2-), not HOOC-COOH<br>
><br>
> 2) Why not to use topology of charged ASP residue side chaas starting point?<br>
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><br>
> ------------------------------<br>
><br>
> Message: 5<br>
> Date: Wed, 28 Oct 2009 20:19:53 -0400<br>
> From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
> Subject: Re: [gmx-users] em ok, md wrong<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
> Message-ID: <<a href="mailto:4AE8DFA9.4000904@vt.edu" target="_blank">4AE8DFA9.4000904@vt.edu</a>><br>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
><br>
><br>
><br>
> Yuri Garmay wrote:<br>
> > 2009/10/28 Liliya Shamova <<a href="mailto:lshamova@yahoo.com" target="_blank">lshamova@yahoo.com</a> <mailto:<a href="mailto:lshamova@yahoo.com" target="_blank">lshamova@yahoo.com</a>>><br>
> ><br>
> > Hi everybody!<br>
> ><br>
> ><br>
> > Dihedrals seem be incorrect. Check it. (I don't know what have to be, is<br>
> > it planar molecule or not, it have be known, but it seems to be<br>
> > incorrect, as you say molecule distorted) Additionally, you should use<br>
> > improper dihedrals for making planar parts.<br>
> ><br>
><br>
> Indeed, the dihedrals don't make much sense. Based on ASPH, you should define a<br>
> HO-OH-C-O dihedral for each carboxylic acid group, and I would think you would<br>
> also need to define an O-C-C-O torsion. All of this information is in the<br>
> ffoplsaabon.itp and ffoplsaa.rtp files. You should definitely define impropers<br>
> to keep the carboxylic acid groups planar. Using the ASPH entry in ffoplsaa.rtp<br>
> is a good start. If hydrogens are collapsing into neighboring acid groups, your<br>
> [pairs] directive is probably incorrect.<br>
><br>
> > P.S.<br>
> ><br>
> > 1) I think, this acid is charged in neutral pH. OOC-COO (2-), not HOOC-COOH<br>
><br>
> True, but this is (as described) a vacuum simulation, so we're not dealing with<br>
> solution pH.<br>
><br>
> -Justin<br>
><br>
> ><br>
> > 2) Why not to use topology of charged ASP residue side chaas starting point?<br>
> ><br>
> ><br>
> > ------------------------------------------------------------------------<br>
> ><br>
> > _______________________________________________<br>
> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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> > Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> > Please don't post (un)subscribe requests to the list. Use the<br>
> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
> > Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
</blockquote></div><br>
</div></div></blockquote></div><br></div></div></div>
</blockquote></div><br></div>