[gmx-users] set up topology in free energy calculations
friendli2000 at gmail.com
Thu Apr 3 08:20:48 CEST 2008
Dear Gmx users,
I am calculating the mutation free energy from amino acid Asp to Asn as
a test job for my practice.
I have some questions about setting up the topology file.
1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or
simply -OH to -NH2.
In topology, O <-> N.
What about the hydrogens, do I need one or two dummy(DUM) atoms?
a), DUM <-> H ; H(of OH) <-> H(of NH2)
b), DUM <-> H(of NH2); DUM <-> H(of NH2); H(of OH) to DUM
a) or b) should I use?
2, I need to provide the coordinates for the dummy atoms in the .gro
file(Asp), right? since otherwise the # of atoms in .top and .gro will
3, from the tutorial(methane) I read, the masses of the dummy atom keeps
like real atom and the C6 and C12 changes to zero in [atomtypes] to
vanish the nonbonded interactions. How to deal with the bonds and the
charges for dummy atoms? bonded interactions?
I think I am a bit confused by the definition of the dummy atom. I
understanding is a dummy atom is a atoms with same mass but no
interaction with all other atoms. Is that right?
thanks for help and suggestions are appreciate.
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