<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
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>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 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 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 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 files<br>> > I've told you (posre_A.itp, posre_B.itp and posre_C.itp), grompp needs a<br>> > posre.itp file. So the solution was to create a empty posre.itp file.<br>> > Now it's clear to me that my first option (see below the description of<br>> > the first posre.itp file I've created) makes no sense because by that<br>> > way I was calling each posre_*.itp file twice: once in the .top 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 work.<br>> > <br>> <br>> Well, I'm glad it worked, but having to create an empty posre.itp file sounds a <br>> bit nonsensical to me. Maybe the developers can help us out - has something <br>> within grompp changed that makes a posre.itp file explicitly 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 atoms,<br>> >>> respectively. In the last line of each .itp file I have 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 within an .itp <br>> >> file. That may work, but I've never tried it. Each .itp file should provide <br>> >> the parameters for a single molecule, no more. What I would try 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 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 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 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 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 4.0<br>> >>> demands a posre.itp file, an so I've created this one, and at 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 different<br>> >>> systems, in two different simulations, I get the same error in 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 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 to.<br>> >>>>> In that case move the "position_restraints" section to the right<br>> >>>>> molecule.<br>> >>>>> -------------------------------------------------------<br>> >>>>><br>> >>>>><br>> >>>>> I'm not understanding why is "Atom index (15)" out of bounds. The range<br>> >>>>> (1-14), where did it came from?<br>> >>>> grompp is finding a 15th atom to which it is trying to apply position<br>> >>>> restraints, but it is unable to.<br>> >>>><br>> >>>>> It seems that I just can only have 14 position_restaints conditions, but<br>> >>>>> this don't make any sense to me. Can anyone help with this? What do I<br>> >>>>> have to do to solve this problem?<br>> >>>>><br>> >>>> The error message is pretty clear - you have inserted #include "posre.itp"<br>> >>>> within the incorrect molecule definition (i.e., it is in the 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 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>> >>>> ========================================<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 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 /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
</html>