[gmx-users] how to modify the peptide end groups??

Marco Ceruso mceruso at physbio.mssm.edu
Tue Aug 19 20:07:00 CEST 2003

pdb2gmx will add the end groups for you without any need to modify .rtp

-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Vivek Raut
Sent: Tuesday, August 19, 2003 1:41 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] how to modify the peptide end groups??


i want to change the end groups of GLY (glycine) segment to NH3+ & COO- . I
tried to modify the ffgmx2.rtp file by adding hydrogens & oxygen as per the
atom type defined in ffgmx2.atp. But when i try to make a .gro file for the
peptide, it says that its not abel to match the hydrogens from .hdb &. tdb

is there a more logical way to modify the end groups?

if not, then how to modify the .hdb & .tdb files??

Vivek Raut
Graduate Research Assistant
Department of Bioengineering
Clemson University
Clemson, SC- 29631. USA
Email: vraut at clemson.edu
Phone: 864-650-1431

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