[gmx-users] amb2gmx for big systems

Rebeca García Fandiño regafan at hotmail.com
Thu Jul 31 20:17:12 CEST 2008

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:
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
However, several atomtypes for the lipid are the same than those for the protein, and they have nothing to do between them:
[ atomtypes ];name  bond_type    mass    charge   ptype          sigma      epsilonO              O      0.0000  0.0000  A   2.95992e-01  8.78640e-01H1            H1      0.0000  0.0000  A   2.64953e-01  6.56888e-02N3            N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01O2            O2      0.0000  0.0000  A   2.95992e-01  8.78640e-01HA            HA      0.0000  0.0000  A   2.64953e-01  6.56888e-02HC            HC      0.0000  0.0000  A   2.64953e-01  6.56888e-02C              C      0.0000  0.0000  A   3.39967e-01  3.59824e-01CT            CT      0.0000  0.0000  A   3.39967e-01  4.57730e-01HP            HP      0.0000  0.0000  A   2.64953e-01  6.56888e-02
and I am getting errors in grompp due to this fact.
Does anybody has any idea to solve this?
Thank you very much for your help in advance.
Rebeca García Fandiño
Parc Cientific de Barcelona
regafan at hotmail.com
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