[gmx-users] regarding dimethylated lysine topology file

[Justin A. Lemkul]

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.

-Justin

> thanx in advance
> 
> PRASUN (ASHOKA)
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================