[gmx-users] Error with polymer surface modeling

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 1 12:14:47 CEST 2008

h a wrote:
> Dear users,
> I'm working on simulating protein interactions with polymer surface for
> tissue engineering applications.
> I have developed a primitive model of polymer surface of polystyrene using
> "genconf". I have obtained .gro and .itp files using prodrg. But now I
> face  error when I use grompp though I included the .itp in .top file! It
> says "atomtype CR61 is not found". Now I'm struck at this point from many
> days.

So where would one go to find an atomtype?  If you were to enter your 
$GMXLIB directory and 'grep CR61 *' it will print out all the 
occurrences of this atom type.  It will tell you what force field it 
belongs to and what the atom type is.


> Is it that I should add atom types to the ffG43a1nb.itp and ffG43a1bon.itp ? 
> But then where should I get different parameters.  
> Thank you for your help.
> Harshith Asuri, 
> 3rd year UG student 
> IIT Kanpur,
> http://home.iitk.ac.in/~harshith <http://home.iitk.ac.in/%7Eharshith>
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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