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Hi,<br><br>I just ran grompp and it does not complain about anything (and no posre.itp file).<br><br>Are you really sure there is no reference to posre.itp in your files?<br>Try:<br>grep posre *.itp *.top<br><br>Berk<br><br><br>> Subject: RE: [gmx-users] Problems with grompp and posre.itp in gromacs 4.0<br>> From: nazoia@det.uminho.pt<br>> To: gmx-users@gromacs.org<br>> Date: Wed, 5 Nov 2008 15:53:16 +0000<br>> <br>> On Wed, 2008-11-05 at 16:28 +0100, Berk Hess wrote:<br>> > Hi,<br>> > <br>> > I just ran the 4.0 version of pdb2gmx on a multi-chain pdb file<br>> > and posre.itp does not appear anywhere.<br>> <br>> When I've run pdb2gmx on my multi-chain pdb file I get posre_*.itp files<br>> automatically because in my pdb file I have chain identifiers; I have<br>> chain A and chain B, and Gromacs assumed chain C. That files was not<br>> "hand made".<br>> <br>> Now I've tried to run pdb2gmx on the same pdb file, but without chain<br>> identifiers and I get just one posre.itp file with all the information.<br>> <br>> But the real question is not that. Why is grompp asking for a posre.itp<br>> file that's not declared anywhere? In the .top file I declared my<br>> posre_*.itp files, so why is grompp ask me for posre.itp? And the<br>> strange thing is that with a empty file everything is working now.<br>> <br>> Have you tried to run energy minimization on multi-chain system, having<br>> no posre.itp file?<br>> <br>> Nuno Azoia<br>> <br>> > <br>> > From the file names it seems that the files are non-standard<br>> > and made of modified by hand.<br>> > So maybe you somehow modified a file with posre.itp in it?<br>> > <br>> > Berk<br>> > <br>> > <br>> > > Date: Wed, 5 Nov 2008 10:11:03 -0500<br>> > > From: jalemkul@vt.edu<br>> > > To: nazoia@det.uminho.pt; gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Problems with grompp and posre.itp in<br>> > gromacs 4.0<br>> > > CC: <br>> > > <br>> > > <br>> > > <br>> > > Nuno Azoia wrote:<br>> > > > On Wed, 2008-11-05 at 07:57 -0500, Justin A. Lemkul wrote:<br>> > > >> Please remember to keep all correspondence on the list for<br>> > archiving purposes. <br>> > > >> Also, others out there may have information to contribute.<br>> > > > <br>> > > > Sorry about that. I just press Reply and I didn't check the e-mail<br>> > > > address.<br>> > > > <br>> > > > I've solved the problem with your help.<br>> > > > <br>> > > > I've tried what you have told me but I get the same error message.<br>> > > > Calling an .itp file within a .itp file always works with me (in<br>> > version<br>> > > > 3.3.1), but it makes more sense the way you describe, declaring<br>> > > > everything in the .top file.<br>> > > > <br>> > > > The problem seems to be the posre.itp file itself. Even with the 3<br>> > files<br>> > > > I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp<br>> > needs a<br>> > > > posre.itp file. So the solution was to create a empty posre.itp<br>> > file.<br>> > > > Now it's clear to me that my first option (see below the<br>> > description of<br>> > > > the first posre.itp file I've created) makes no sense because by<br>> > that<br>> > > > way I was calling each posre_*.itp file twice: once in the .top<br>> > file and<br>> > > > the other in posre.itp file. Grommp was reading the posre.itp file<br>> > > > first, without any reference to any molecule, and it just don't<br>> > work.<br>> > > > <br>> > > <br>> > > Well, I'm glad it worked, but having to create an empty posre.itp<br>> > file sounds a <br>> > > bit nonsensical to me. Maybe the developers can help us out - has<br>> > something <br>> > > within grompp changed that makes a posre.itp file explicitly<br>> > necessary?<br>> > > <br>> > > -Justin<br>> > > <br>> > > > Thank you very much!<br>> > > > <br>> > > > Nuno Azoia<br>> > > > <br>> > > >> Nuno Azoia wrote:<br>> > > >>> Hi Justin. Tank you for your answer!<br>> > > >>><br>> > > >>> Ok! I agree with you, and I'm doing something wrong. I just can<br>> > > >>> understand what. Can you please help me a little more.<br>> > > >>><br>> > > >>> In my .top file I have this lines<br>> > > >>><br>> > > >>> -----------------------------------------------------------<br>> > > >>> ; Include chain topologies<br>> > > >>> #include "krt_spd_C.itp"<br>> > > >>> #include "krt_spd_A.itp"<br>> > > >>> #include "krt_spd_B.itp<br>> > > >>> -----------------------------------------------------------<br>> > > >>><br>> > > >>><br>> > > >> That should be fine.<br>> > > >><br>> > > >>><br>> > > >>> The krt_spd_C.itp is the topology of a peptide with 244 atoms.<br>> > > >>> krt_spd_A.itp and krt_spd_B.itp are peptides with 435 and 418<br>> > atoms,<br>> > > >>> respectively. In the last line of each .itp file I have<br>> > something like<br>> > > >>> this (the letter changes with the corresponding file name)<br>> > > >>><br>> > > >>> -----------------------------------------------------------<br>> > > >>> ; Include Position restraint file<br>> > > >>> #ifdef POSRES<br>> > > >>> #include "posre_A.itp"<br>> > > >>> #endif<br>> > > >>> -----------------------------------------------------------<br>> > > >>><br>> > > >>><br>> > > >> This might be the problem. You're calling an .itp file from<br>> > within an .itp <br>> > > >> file. That may work, but I've never tried it. Each .itp file<br>> > should provide <br>> > > >> the parameters for a single molecule, no more. What I would try<br>> > is the following:<br>> > > >><br>> > > >> ; Include chain topologies<br>> > > >> #include "krt_spd_C.itp"<br>> > > >><br>> > > >> #ifdef POSRES_C<br>> > > >> #include "posre_C.itp"<br>> > > >> #endif<br>> > > >><br>> > > >> #include "krt_spd_A.itp"<br>> > > >><br>> > > >> #ifdef POSRES_A<br>> > > >> #include "posre_A.itp"<br>> > > >> #endif<br>> > > >><br>> > > >> #include "krt_spd_B.itp"<br>> > > >><br>> > > >> #ifdef POSRES_B<br>> > > >> #include "posre_B.itp"<br>> > > >> #endif<br>> > > >><br>> > > >> That way, each chain topology is followed by its corresponding<br>> > position <br>> > > >> restraint file, under the appropriate [ molecule ] definition.<br>> > > >><br>> > > >> -Justin<br>> > > >><br>> > > >>><br>> > > >>> Each posre_*.itp file has positions restraints for all the atoms<br>> > in the<br>> > > >>> peptide. For instance, posre_A.itp is something like this:<br>> > > >>><br>> > > >>> -----------------------------------------------------------<br>> > > >>> ; In this topology include file, you will find position<br>> > restraint<br>> > > >>> ; entries for all the heavy atoms in your original pdb file.<br>> > > >>> ; This means that all the protons which were added by pdb2gmx<br>> > are<br>> > > >>> ; not restrained.<br>> > > >>><br>> > > >>> [ position_restraints ]<br>> > > >>> ; atom type fx fy fz<br>> > > >>> 1 1 1000 1000 1000<br>> > > >>> 5 1 1000 1000 1000<br>> > > >>> 6 1 1000 1000 1000<br>> > > >>> (...)<br>> > > >>> 430 1 1000 1000 1000<br>> > > >>> 433 1 1000 1000 1000<br>> > > >>> 434 1 1000 1000 1000<br>> > > >>> 435 1 1000 1000 1000<br>> > > >>> ------------------------------------------------------------<br>> > > >>><br>> > > >>><br>> > > >>><br>> > > >>><br>> > > >>> Ok. In version 3.3.1 that's all I used to do. But now version<br>> > 4.0<br>> > > >>> demands a posre.itp file, an so I've created this one, and at<br>> > least by<br>> > > >>> this way grompp are reading my files<br>> > > >>><br>> > > >>> ------------------------------------------------------------<br>> > > >>> ; Include posre topology<br>> > > >>> #include "posre_A.itp"<br>> > > >>> #include "posre_B.itp"<br>> > > >>> #include "posre_C.itp"<br>> > > >>> ------------------------------------------------------------<br>> > > >>><br>> > > >>><br>> > > >>><br>> > > >>><br>> > > >>> That's why I can not understand what I'm doing wrong.<br>> > > >>><br>> > > >>> Another thing that I'm finding surprising is that, with two<br>> > different<br>> > > >>> systems, in two different simulations, I get the same error in<br>> > the 15th<br>> > > >>> position.<br>> > > >>><br>> > > >>> Thank you for your time.<br>> > > >>><br>> > > >>> Nuno Azoia<br>> > > >>><br>> > > >>><br>> > > >>><br>> > > >>> On Tue, 2008-11-04 at 13:14 -0500, Justin A. Lemkul wrote:<br>> > > >>>> Quoting Nuno Azoia <nazoia@det.uminho.pt>:<br>> > > >>>><br>> > > >>>>> Hi!<br>> > > >>>>><br>> > > >>>>> I'm having problems with grompp in version 4.0.<br>> > > >>>>> When I attempt to run grompp I get this message. I've tried<br>> > with two<br>> > > >>>>> different systems, but the message is exactly the same<br>> > > >>>>><br>> > > >>>>> -------------------------------------------------------<br>> > > >>>>> Program grompp, VERSION 4.0<br>> > > >>>>> Source code file: toppush.c, line: 1196<br>> > > >>>>><br>> > > >>>>> Fatal error:<br>> > > >>>>> [ file posre_A.itp, line 16 ]:<br>> > > >>>>> Atom index (15) in position_restraints out of bounds (1-14).<br>> > > >>>>> This probably means that you have inserted topology section<br>> > > >>>>> "position_restraints"<br>> > > >>>>> in a part belonging to a different molecule than you intended<br>> > to.<br>> > > >>>>> In that case move the "position_restraints" section to the<br>> > right<br>> > > >>>>> molecule.<br>> > > >>>>> -------------------------------------------------------<br>> > > >>>>><br>> > > >>>>><br>> > > >>>>> I'm not understanding why is "Atom index (15)" out of bounds.<br>> > The range<br>> > > >>>>> (1-14), where did it came from?<br>> > > >>>> grompp is finding a 15th atom to which it is trying to apply<br>> > position<br>> > > >>>> restraints, but it is unable to.<br>> > > >>>><br>> > > >>>>> It seems that I just can only have 14 position_restaints<br>> > conditions, but<br>> > > >>>>> this don't make any sense to me. Can anyone help with this?<br>> > What do I<br>> > > >>>>> have to do to solve this problem?<br>> > > >>>>><br>> > > >>>> The error message is pretty clear - you have inserted #include<br>> > "posre.itp"<br>> > > >>>> within the incorrect molecule definition (i.e., it is in the<br>> > wrong order or<br>> > > >>>> wrong section in the .top).<br>> > > >>>><br>> > > >>>> -Justin<br>> > > >>>><br>> > > >>>>> Tank you<br>> > > >>>>><br>> > > >>>>> Nuno Azoia<br>> > > >>>>><br>> > > >>>>> --<br>> > > >>>>><br>> > > >>>>> Nuno Gonçalo Azoia Lopes<br>> > > >>>>><br>> > > >>>>> Laboratório de Investigação em Acabamento<br>> > > >>>>> Departamento de Engenharia Textil<br>> > > >>>>> Universidade do Minho<br>> > > >>>>> Campus de Azurém<br>> > > >>>>> 4800-058 Guimarães<br>> > > >>>>> Portugal<br>> > > >>>>><br>> > > >>>>> Tel: +351 253 510 280 - Ext: 517 289<br>> > > >>>>> Fax: +351 253 510 293<br>> > > >>>>><br>> > > >>>>> Mobile: +351 965 382 487<br>> > > >>>>> E-mail: nazoia@det.uminho.pt<br>> > > >>>>><br>> > > >>>>> _______________________________________________<br>> > > >>>>> gmx-users mailing list gmx-users@gromacs.org<br>> > > >>>>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > >>>>> Please search the archive at http://www.gromacs.org/search<br>> > before posting!<br>> > > >>>>> Please don't post (un)subscribe requests to the list. Use the<br>> > > >>>>> www interface or send it to gmx-users-request@gromacs.org.<br>> > > >>>>> Can't post? Read<br>> > http://www.gromacs.org/mailing_lists/users.php<br>> > > >>>>><br>> > > >>>><br>> > > >>>> ========================================<br>> > > >>>><br>> > > >>>> Justin A. Lemkul<br>> > > >>>> Graduate Research Assistant<br>> > > >>>> Department of Biochemistry<br>> > > >>>> Virginia Tech<br>> > > >>>> Blacksburg, VA<br>> > > >>>> jalemkul@vt.edu | (540) 231-9080<br>> > > >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<br>> > > >>>><br>> > > >>>> ========================================<br>> > > >>><br>> > > > <br>> > > > <br>> > > <br>> > > -- <br>> > > ========================================<br>> > > <br>> > > Justin A. Lemkul<br>> > > Graduate Research Assistant<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > > <br>> > > ========================================<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before<br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the <br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > <br>> > ______________________________________________________________________<br>> > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? 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