Amanda Watkins wrote:
I am trying to create a .gro file of a single detergent which I am going
to then multiply and put it in water and have it form micelles. In order
to create a .gro file, I know I need to create a .rtp file of my residue
You do not *need* a .gro file, nor do you necessarily have to produce it using
pdb2gmx.
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file
You do, however, need a topology, so pdb2gmx is one approach, yes.
or add it to the desired force field .rtp file I want to run my
detergent in. Is there any way to custom make one (or add it to an
existing .rtp) using data that I took from another program that I used
to analyze and minimize my detergent? I am currently trying to create a
Certainly. See the manual for the .rtp file format specifications, or write the
topology by hand. Chapter 5 of the manual is a must-read.
.rtp and a .top file using x2top, but that still might not enable me to
generate a .gro file. Thank you for taking the time to read my email and
help me answer my question.
Does x2top give you a topology, though? That's the hard part. See the above
link regarding .gro files.
-Justin
--
========================================
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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