Hello > > I have to question. > 1- I am generating a gro and toplogy file from a pdb file, usign pdb2gmx. > the pdb file contains 18 separate chains, in each chain, there are 6 > residues. > 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 ... > > is it normal? > 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? > > 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: > > Generated 2211 of the 2211 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 0.5 > Generated 2211 of the 2211 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein' > Excluding 3 bonded neighbours molecule type 'Protein2' > Excluding 3 bonded neighbours molecule type 'Protein3' > Excluding 3 bonded neighbours molecule type 'Protein4' > Excluding 3 bonded neighbours molecule type 'Protein5' > Excluding 3 bonded neighbours molecule type 'Protein6' > Excluding 3 bonded neighbours molecule type 'Protein7' > Excluding 3 bonded neighbours molecule type 'Protein8' > Excluding 3 bonded neighbours molecule type 'Protein9' > Excluding 3 bonded neighbours molecule type 'Protein10' > Excluding 3 bonded neighbours molecule type 'Protein11' > Excluding 3 bonded neighbours molecule type 'Protein12' > Excluding 3 bonded neighbours molecule type 'Protein13' > Excluding 3 bonded neighbours molecule type 'Protein14' > Excluding 3 bonded neighbours molecule type 'Protein15' > Excluding 3 bonded neighbours molecule type 'Protein16' > Excluding 3 bonded neighbours molecule type 'Protein17' > Excluding 3 bonded neighbours molecule type 'Protein18' > Excluding 2 bonded neighbours molecule type 'SOL' > > what is this telling me? I didn't find a solution searching in the mailing > list?! > > Thanks > Fahimeh >
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