[gmx-users] Do I need to add hydrogens?
vraut at CLEMSON.EDU
Wed Jan 21 22:04:01 CET 2004
I am trying to introduce a new molecule in gromacs residue topology
database. The molecular structure is:
In order to get this molecule recognized by gromacs, I have added the
following part in ffgmx2.rtp file.
[ atoms ]
OA OA 0.000 0
C2 C2 0.000 1
C3 C2 0.000 2
C4 C2 0.000 3
C5 C2 0.000 4
C6 C2 0.000 5
C7 C2 0.000 6
C8 C2 0.000 7
C9 C2 0.000 8
C10 C3 0.000 9
[ bonds ]
Thus in gromacs terms, the molecule will look like
To make this addition I took the decane molecule, which is already present
in gromacs residue file, as a guideline.
I have 2 questions on this:
1: it is ok NOT to include hydrogens in the .rtp file as well as .pdb file
while making a molecule? ( as there were no hydrogens included in Decane &
I suppose gromacs automatically adds the hydrogens to complete the
molecules). Is it ALLOWED in gromacs?
2: Am I doing something wrong in introducing a new molecule to gromacs by
adding something in .rtp file?
3: If I have to add hydrogens, wont the .rtp file be too complicated after
including all the hydrogen bonds, angles & dihedrals?. What can be done in
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