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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. <b> Once you #include a new molecule, you start a new <br>[moleculetype] entry and the position restraints belong to it. </b> <br> <br><br>So I rechecked my .top file and found that [moleculetype] only occurs once. Perhaps I have misunderstood you. So I added the top file below. I did not add the contents of [atoms] [bonds] etc because I felt the mail 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><hr>Hotmail: Trusted email with Microsoft’s powerful SPAM protection. <a href="https://signup.live.com/signup.aspx?id=60969">Sign up now.</a> <br /><hr />Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. <a href='https://signup.live.com/signup.aspx?id=60969' target='_new'>Sign up now.</a></body>
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