[gmx-users] cholesterol

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 21 13:43:31 CEST 2011

On 4/21/2011 8:05 PM, Preeti Gupta wrote:
> Hi All,
> I am new user of gromacs and i want to simulate cholesterol + DOPC as 
> my final year project.
> firstly i tried gromacs with cholesterol, for which i have downloaded 
> cholesterol pdb and itp file from gromacs site by Monika Hoeltje.
> i m getting the following error- Residue 'CHOL' not found in residue 
> topology database.

... which you need if only if you want to use pdb2gmx on a structure file.

> I tried PRODRG for generating cholesterol topology file and coordinate 
> file, but still i got the error-
> invalid directive of atomtype.

So you've got some file format wrong...

> can someone give me charmm residue topology file for cholesterol or 
> with some solution.

I think you will profit from doing some tutorial material and looking at 
the examples in chapter 5 of the manual.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110421/29e73e75/attachment.html>

More information about the gromacs.org_gmx-users mailing list