[gmx-users] Do I need to add hydrogens?

Vivek Raut 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 ]
     OA    C2
     C2    C3
     C3    C4
     C4    C5
     C5    C6
     C6    C7
     C7    C8
     C8    C9
     C9    C10

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 
this case?

thank you.


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