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<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr">Hello<br><br>I have to question.<br>1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. <br>
the pdb file contains 18 separate chains, in each chain, there are 6 residues.<br>When I generate the topology and coordinates, it creates 18 posres-protein$i.itp file and 18 topol-protein$i.itp file and then one topol.top and one conf.gro ...<br>
<br>is it normal? <br>i think it is just the position restraint for separate chains ... in this way i think it enables me to restraint them separately if i want? right?<br><br>2- using topol.top and conf.gro, after solvating the molecule in the box of water ... with editconf and genbox ... I am trying to generate a tpr file, but when it generate it writes the following:<br>
<br>Generated 2211 of the 2211 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2211 of the 2211 1-4 parameter combinations<br>Excluding 3 bonded neighbours molecule type 'Protein'<br>
Excluding 3 bonded neighbours molecule type 'Protein2'<br>Excluding 3 bonded neighbours molecule type 'Protein3'<br>Excluding 3 bonded neighbours molecule type 'Protein4'<br>Excluding 3 bonded neighbours molecule type 'Protein5'<br>
Excluding 3 bonded neighbours molecule type 'Protein6'<br>Excluding 3 bonded neighbours molecule type 'Protein7'<br>Excluding 3 bonded neighbours molecule type 'Protein8'<br>Excluding 3 bonded neighbours molecule type 'Protein9'<br>
Excluding 3 bonded neighbours molecule type 'Protein10'<br>Excluding 3 bonded neighbours molecule type 'Protein11'<br>Excluding 3 bonded neighbours molecule type 'Protein12'<br>Excluding 3 bonded neighbours molecule type 'Protein13'<br>
Excluding 3 bonded neighbours molecule type 'Protein14'<br>Excluding 3 bonded neighbours molecule type 'Protein15'<br>Excluding 3 bonded neighbours molecule type 'Protein16'<br>Excluding 3 bonded neighbours molecule type 'Protein17'<br>
Excluding 3 bonded neighbours molecule type 'Protein18'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>what is this telling me? I didn't find a solution searching in the mailing list?!<br>
<br>Thanks<br><font color="#888888">Fahimeh<br>
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