[gmx-users] gromacs bond type

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 13 12:41:40 CEST 2008

prasun kumar wrote:
> dear users,
> I am trying to get some information about the bond type,angle type and 
> dihedral angle type.
> can any one please tell me what is the bond type of C-F.angle type for 
> F-C-F,dihedral angle type of F-C-C-O &F-C-C-H.
> Or any one can tell me how to define the gromacs type for bonds,angles.I 
> tried to read the 5th chapter but not getting any thing.

As I told you several emails ago, you can find templates for all of this type of 
information in the tfe.itp that is provided with the Gromacs distribution.  Even 
if you're not looking to use these exact parameters (i.e., if you're making 
changes or refining the model), it's the place to start!  All necessary bonded 
terms are defined for you already.

> actually i am lookig forward to include TFE in the rtp file for my 
> simulation of peptide in TFE.

There are already .rtp entries in the newer Gromos96 force fields for TFE, 
although I don't know why one would need to include it in an .rtp.  As Tsjerk 
told you several emails ago, the .rtp file is for reading building blocks into 
pdb2gmx.  You would not need to run pdb2gmx on a solvent box, or on a 
peptide/protein/whatever in TFE; just #include the appropriate .itp file for the 
solvent and you're done!


> Please help me.
> Thanx in advance
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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