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Hello,<BR>
I am trying to translate the amber topology for a system membrane+protein (dry) to Gromacs. In view of the problems caused in amb2gmx.pl due to the size of the system (more than 600.000 atoms) I had tried another alternative:<BR>
I created the amber topology for the protein and for a unique lipid molecule separately and I converted them to gromacs using amb2gmx.pl (now, no problems were found, as is logic). Then, from the gromacs topologies, I construct the .itp files for the protein and lipid, removing the correspondent lines and putting them into another file that I have called amberff.itp<BR>
<BR>
However, several atomtypes for the lipid are the same than those for the protein, and they have nothing to do between them:<BR>
<BR>
[ atomtypes ]<BR>;name bond_type mass charge ptype sigma epsilon<BR>O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01<BR>H1 H1 0.0000 0.0000 A 2.64953e-01 6.56888e-02<BR>N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01<BR>O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01<BR>HA HA 0.0000 0.0000 A 2.64953e-01 6.56888e-02<BR>HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02<BR>C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01<BR>CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01<BR>HP HP 0.0000 0.0000 A 2.64953e-01 6.56888e-02<BR>
<BR>
and I am getting errors in grompp due to this fact.<BR>
<BR>
Does anybody has any idea to solve this?<BR>
<BR>
Thank you very much for your help in advance.<BR>
<BR>
Rebeca García Fandiño<BR>
Parc Cientific de Barcelona<BR>
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