[gmx-users] editing parameters

Paul Barrett barrett at biop.ox.ac.uk
Thu May 8 09:55:02 CEST 2003

 From memory here is what I think I did when trying to do the same for
another non standard residue:

1) Find your .rtp file. It will be somewhere like

In that folder are lots of files of which about 5 have the extension
.rtp. Find the on that corresponds the the force field parameters that
you plan to use (e.g.I am using ffG43a1.rtp)

2) Having made a backup of the existing .rtp file use any editor to open
the file and add in your residue. This is documented pretty well in the
manual (section 5.5.1 in my version). This is the part that takes a bit
of time. I suggest you start with a very simple version e.g. a test
residue with 5 atoms in it and make sure you can make that work.

3) You may also need to add an entry in the hydrogen database (.hdb) for
that residue depending on your subsequent protocol.

If you have any non standard atoms you will have to add them into the
corresponding .atp file

hope that starts you in the right direction

Paul Barrett
University of Oxford
Department of Biochemistry
barrett at biop.ox.ac.uk

>I am setting up a run to do a MD calculation, which includes a ligand 
>(ethidium cation) that pdb2gmx doesn't recognize.  Ethidium doesn't 
>contain any oddly-parameterized atom types.  I have used gaussian to 
>calculate the ethidium charges, but am not sure how to import those 
>charges into the parameter files. Various error messages received while 
>trying to run pdb2gmx have been (depending on force field tried):
>Fatal error: Atom C1 in residue ETH not found in rtp database   **OR**
>Fatal Error: Residue "ET" not found in residue topology database
>as examples.
>What is the procedure for editing the rtp ?
>Regina Monaco
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