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

[Marco Ceruso]

  -----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 3:27 PM
  To: gmx-users at gromacs.org
  Subject: [gmx-users] how to make end groups charged??


  but by default, it makes the end groups NH2 & COOH. I want to make it
charged,  what modifications are needed?
  [Marco Ceruso]
  pdb2gmx -f conf.gro -ter  and you should be given a choice of terminii




  >>>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??

   hi,
   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??


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  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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