<p>Sir thanx for the reply,<br /> I have a hydrogen.pdb file which I have generated from chem sketch.<br /><font size="2"><br />HETATM 1 H1 HYD 1 -0.353 -0.022 -0.013 1.00 0.00 H<br />HETATM 2 H2 HYD 1 0.353 0.022 0.013 1.00 0.00 H<br />CONECT 1 2<br />CONECT 2 1<br />END<br />I am using genboc -ci option to insert 100 hydrogen molecules in the solvated box containing water and protein.<br />Now the topology file "hydrogen.itp" I am using definig hydrogen as a 3 point molecule.<br /><font size="2"><font size="3"><em><font size="2">
<p>[ moleculetype ]<br />; molname nrexcl<br />HYD 2<br />[ atoms ]<br />; nr type resnr residue atom cgnr charge mass<br />#ifdef _FF_OPLS <br /> 1 opls_966 1 HYD H1 1 0.475<br /> 2 opls_967 1 HYD H2 1 0.475<br /> 3 opls_968 1 HYD DH 1 -0.950<br />#endif<br /><br />[dummies2]<br />;Dummy from from funct a<br /> 3 1 2 1 0.5</p>
<p>I am confused if the pdb should also contain the dummy atom.<br />Kindly give me a example as the theory in manual is little bit compact<br /><br />Thanking you<br />Vipul<br /><br /> </p></font></em></font></font></font></p>
<p>[ moleculetype ]<br />; molname nrexcl<br />HYD 2<br />[ atoms ]<br />; nr type resnr residue atom cgnr charge mass<br />#ifdef _FF_OPLS <br /> 1 opls_966 1 HYD H1 1 0.475<br /> 2 opls_967 1 HYD H2 1 0.475<br /> 3 opls_968 1 HYD DH 1 -0.950<br />#endif<br /><br />[dummies2]<br />;Dummy from from funct a<br /> 3 1 2 1 0.5</p>
<p>I am confused if the pdb should also contain the dummy atom.<br />Kindly give me a example as the theory in manual is little bit compact<br /><br />Thanking you<br />Vipul<br /><br /> </p><br>