On 10/5/12 10:39 AM, vidhya sankar wrote:
Thank you Justin For Your Previous reply
Finally Somehow I have Adjusted The Cut-Off and Grid Size and Inserted
Protein in Lipid By Deleting some Lipid Molecules MY Question is
1) When I am
Using inflategro Perl Script ,I need to Use Cut-off , Scaling Factor ,Grid
size ,
Is there is Any Rule to Set up Suitable Factor (Aforesaid) For my System ?
Please read the paper associated with the InflateGRO script.
2) I need to Use Only Protein Surrounded By Lipid Molecules . I Do not Want
to use genion tool to insert water .
Is it Possible ? and Is it Reasonable To do Direct Minimization,
Equilibration, Production MD without Water ?
You can do EM without water, but trying to simulate a protein in a membrane in
vacuum does not make sense. The force fields are not designed to be used in
this way.
-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
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