Liu, Liang wrote:
This is a "reasonable" answer :)
Thanks for that, and I just tried Gromacs for minimization, and looks
the final structure does not have clashes anymore, and also are very
close to the initial structure.
Another question is if there is a way to add ions automatically, meaning
no need to check the "NOTE" of "System has non-zero total charge" in the
output of grompp command? And also update the topology file
automatically too?
That depends on the system. For a simple solute in water, the running total
charge of the solute is recorded in the qtot column of the .top file. If you
have a complex system with lots of charged things, no, there is no convenient
way to get the charge aside from calculating it by hand or reading the grompp
output.
The topology can be modified automatically by genion after ions are added by
using the -p flag.
-Justin
On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Liu, Liang wrote:
Hi, all,
I am wondering if Gromacs can do the following work?
Assuming I have a pdb file of an RNA molecule. Some atoms may be
too close or even overlap, I am wondering if Gromacs can move
the atoms to reasonable positions and remove the bad contacts?
The final structure is supposed to be the "most" stable
structure with minimal energy. I know AMBER minimization can do
this work, and I am wondering if Gromacs can do the same?
Gromacs is perfectly capable of energy minimization. Whether or not
minimization succeeds and gives a reasonable output is mostly
dependent upon the feasibility of the starting structure. If the
minimization crashes, it's not Gromacs' fault ;)
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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Liang Liu
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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