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Hi,<br><br>Sorry to bother you again, but I am new to gromacs and many theings don't make sense yet. <br>I have tried reading the manual but I do not understand what you mean by "Note how the automatically-generated "posre.itp" file is #included at
the end of the Protein_A moleculetype, *before* any other
molecules are introduced. You have to do the same with any new #include statements or
directives you add." <br><br>I tried using #include in front of my code for [position_restraints] but that just gives an error. So I suppose that isn't what you mean. <br>Furthermore, in section 5.7.1 of the manual pg110 an example topology file called urea.top is shown. there is no include there.<br><br>In this example .top file they just seem to have added the position restraints they want after the dihedrals. This approach does not seem to be working for me and I can not understand why. <br><br>Thank you again for your help, <br>Abdullah<br><br>> Date: Thu, 3 Jun 2010 09:43:18 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] position restraints<br>> <br>> <br>> <br>> abdullah ahmed wrote:<br>> > Hi!<br>> > <br>> > In your previous mail you mentioned:<br>> > <br>> > The position restraints must belong to the [moleculetype] of<br>> > the species to be restrained. * Once you #include a new molecule, you <br>> > start a new<br>> > [moleculetype] entry and the position restraints belong to it. *<br>> > <br>> > <br>> > So I rechecked my .top file and found that [moleculetype] only occurs <br>> > once. Perhaps I have misunderstood you. So I added the top file below. I <br>> <br>> No it doesn't. Each time you #include a new .itp file, you are telling grompp <br>> to copy and paste the contents of that .itp file in that location. Have a look <br>> at spc.itp - it starts a new moleculetype.<br>> <br>> http://www.gromacs.org/Documentation/Include_File_Mechanism<br>> <br>> Note how the automatically-generated "posre.itp" file is #included at the end of <br>> the Protein_A moleculetype, *before* any other molecules are introduced. You <br>> have to do the same with any new #include statements or directives you add.<br>> <br>> -Justin<br>> <br>> > did not add the contents of [atoms] [bonds] etc because I felt the mail <br>> > would become unnecessarily long.<br>> > <br>> > ; Include forcefield parameters<br>> > #include "ffoplsaa.itp"<br>> > <br>> > [ moleculetype ]<br>> > ; Name nrexcl<br>> > Protein_A 3<br>> > <br>> > [ atoms ]<br>> > <br>> > [ bonds ]<br>> > <br>> > [ pairs ]<br>> > <br>> > [ angles ]<br>> > <br>> > [ dihedrals ]<br>> > <br>> > [ dihedrals ]<br>> > <br>> > ; Include Position restraint file<br>> > #ifdef POSRES<br>> > #include "posre.itp"<br>> > #endif<br>> > <br>> > ; Include water topology<br>> > #include "spc.itp"<br>> > <br>> > #ifdef POSRES_WATER<br>> > ; Position restraint for each water oxygen<br>> > [ position_restraints ]<br>> > ; i funct fcx fcy fcz<br>> > 1 1 1000 1000 1000<br>> > #endif<br>> > <br>> > ; Include generic topology for ions<br>> > #include "ions.itp"<br>> > <br>> > [ system ]<br>> > ; Name<br>> > Protein<br>> > <br>> > [ molecules ]<br>> > ; Compound #mols<br>> > Protein_A 1<br>> > <br>> > Thanks again for your help,<br>> > Abdullah<br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign <br>> > up now. <https://signup.live.com/signup.aspx?id=60969><br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<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://lists.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 />Hotmail: Powerful Free email with security by Microsoft. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Get it now.</a></body>
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