[gmx-users] adding multi-residue molecules in solution

Mark Abraham Mark.Abraham at anu.edu.au
Sat Sep 5 04:12:37 CEST 2009

milad ekramnia wrote:
> Hi dear gromacs users
> how can I insert molecules with more than 1 residue (like a multi-residue protein ) in my box beside the main one  

By having a new [ moleculetype ]. The simplest way to do this is to take 
the secondary molecule and generate a .top file for it using your normal 
method (e.g. pdb2gmx). Then edit that .top file to become an .itp file 
(remove forcefield #include lines, [ default ] section, [ molecules ] 
section) and now you have an .itp file that you can #include into your 
original .top file. Obviously you still need the ordering of your [ 
molecules ] section to match that in your coordinate file.


> and is there a way to set the distance between their Center of masses in the box ? 
> thanks  all

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