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

Vivek Raut vraut at CLEMSON.EDU
Tue Aug 19 19:44:00 CEST 2003


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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