[gmx-users] how to make end groups charged??

Vivek Raut vraut at CLEMSON.EDU
Tue Aug 19 21:29:00 CEST 2003

but by default, it makes the end groups NH2 & COOH. I want to make it 
charged,  what modifications are needed?

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

-----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 files. 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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