[gmx-users] I: How to rolled up a polymer chain

Justin Lemkul jalemkul at vt.edu
Thu Sep 25 14:08:48 CEST 2014

On 9/25/14 4:57 AM, marcello cammarata wrote:
> Hi to all,
> in order to find the position tangled of a polymer chain,
>   i tried to follow the indication of hte page Polymer reported in the gromacs guide on line.
> i created a file oplsaa.rtp and a file oplsaa.hdb as descrived there, and  i save the file on the folder oplsaa, also i created a file PE.pdb as reported in the same page, with the indication for create a chain of polyetilene of 6 monomers, and i saved this last file in the folder ....gromacs/src/

You shouldn't be messing with anything in the src folder; that's the source 
code, not the installed Gromacs.  Nothing you do here will have any effect.

> I start with the command pdb2gmx -f PE.pdb
> i select the force field as 14 OPLS-AA/L
> i select  none as water model (bacause it is a single polymer chain)
> I got the message "residue ethB non found in the residue topology database, aminoacid.r2b"
> I read that the software tried to open other files as aminoacids.rpt aminoacids.hdb and it doen't found the residue.
> A that point i thought to modify the files aminoacids.rpt and aminoacids.rdb by write down what was in the files oplsaa.rtp and oplsaa.hdb in the files aminoacids.rtp and aminoacids.hdb.
> Follow, I run the software with the comand pdb2gmx -f PE.pdb
> wwith same force field and same none water.
> i got the same message:"residue ethB non found in the residue topology database, aminoacid.r2b"
> Questions are:
> how i can do for load that residue?
> What do you suggest to do for induce the software to load my residue?

A few things:

1. The file names in the posted example are outdated, but it should be 
straightforward to see what the new file names are in the reorganized force 
field files.

2. The best approach is not to create files from scratch (especially if you are 
unfamiliar with how all of this works), but rather to extend the existing force 
field.  Make a local copy of the oplsaa.ff directory in your working directory. 
  Add residues to its .rtp file, .hdb entries, etc. as needed in those files. 
Use this modified force field when running pdb2gmx.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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