[gmx-users] regarding dimethylated lysine topology file

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 3 13:12:23 CET 2009

prasun kumar wrote:
> Respected all
> I drew the structure using the drawing tool available in PRODRG server
> then I went for  topology file generation,but the server is deleting 
> almost all the hydrogen atoms while writing the topology file for gromacs
> can any one tell me why it is doing like this?

Because the PRODRG server is for use with the Gromos force fields, which are 
united-atom.  You can get an all-H structure file as output, but the topology is 
force field-dependent.

> another question I got that is
> how to change gromacs topology file to charmm topology file
> (I know for bond length and angle........but for dihedral(improper and 
> proper))

That type of information would be in the Gromacs and CHARMM manuals.

> actually i want toi know which function gromacs is using for the 
> calculation of dihedrals..........

Manual, Chapter 5.


> thanx in advance
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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