[gmx-users] Synthesis of Polyethylene SUrface Topology

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 1 14:31:15 CEST 2010

Yash Gandhi wrote:
> Hi,
> I am a new user of GROMACS and I wish to Generate a Polyethylene Surface 
> for my work related to hydrophobic Surface Properties. I went through an 
> earlier available correspondence 
> <http://lists.gromacs.org/pipermail/gmx-users/2009-March/040125.html> 
> and tried to use the info available. After execution of pdb2gmx command 
> and opting for OPLS force field, I got an error as:
> /
> Fatal error:
> Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
>              while sorting atoms
> /
> I am unable to understand the relevance of this error as in 
> Polyethylene, Alcoholic group is not present whatsoever. Please help me 
> in removing this particular error.

Did you make all the appropriate changes to the .rtp and .hdb files, as 
instructed in the link above?  Right now, pdb2gmx thinks your residues are named 
EtOH (ethanol), so either your coordinate file is named wrong or you haven't 
added the necessary information to the database.


> -- 
> Yash Gandhi,
> 4th Year, BE (Hons) Chemical,
> Birla Institute of Technology & Science, Pilani, India


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list