[gmx-users] Making a .rtp file

[Justin A. Lemkul]

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

-- 
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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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