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 [email protected]
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 [email protected].
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
