On 6/9/12 8:53 AM, ramaraju801 wrote:
@ Mark,
i added -ter to pdb2gmx command and produced the topology file but still the
energy minimization step in vacuum is producing the same error
@justin
am presently running the simulation step i.e energy minimization of
structure in vacuum.
when producing the topology file ,it gave errors saying some of the atoms
are missing in atomtypes which i gave ,
you said atoms shouldn't be added which were not in the first place then can
u tell me the alternative.
Not without the exact error, copied and pasted from the terminal. If you're
working with a simple protein with canonical amino acids, changing an .rtp file
(or anything else in the force field) is never required.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
