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<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> gmx-users-admin@gromacs.org
[mailto:gmx-users-admin@gromacs.org]<B>On Behalf Of </B>Vivek
Raut<BR><B>Sent:</B> Tuesday, August 19, 2003 3:27 PM<BR><B>To:</B>
gmx-users@gromacs.org<BR><B>Subject:</B> [gmx-users] how to make end groups
charged??<BR><BR></FONT></DIV>
<DIV>but by default, it makes the end groups NH2 & COOH. I want to make it
charged, what modifications are needed?<BR><SPAN
class=829440521-19082003><FONT face=Arial color=#0000ff size=2>[Marco
Ceruso] </FONT></SPAN></DIV>
<DIV><SPAN class=829440521-19082003>pdb2gmx -f conf.gro -ter and you
should be given a choice of terminii</SPAN></DIV>
<DIV><SPAN class=829440521-19082003></SPAN><BR><BR><BR><BR>>>>pdb2gmx
will add the end groups for you without any need to modify .rtp etc...
Marc<BR><BR>-----Original Message----- From: <FONT
color=#0000ff><U>gmx-users-admin@gromacs.org</U></FONT> [<A
href="mailto:gmx-users-admin@gromacs.org" eudora="autourl">mailto:</A><A
href="mailto:gmx-users-admin@gromacs.org" eudora="autourl"><FONT
color=#0000ff><U>gmx-users-admin@gromacs.org</A></U></FONT>]On Behalf Of Vivek
Raut Sent: Tuesday, August 19, 2003 1:41 PM To: <FONT
color=#0000ff><U>gmx-users@gromacs.org</U></FONT> Subject: [gmx-users] how to
modify the peptide end groups??<BR><BR> hi,<BR> 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?? <BR><BR></DIV><X-SIGSEP>
<P></X-SIGSEP>-------------------------------------------------------------------------------------------------------------------------------------------<BR>Vivek
Raut<BR>Graduate Research Assistant<BR>Department of Bioengineering<BR>Clemson
University <BR>Clemson, SC- 29631. USA<BR>Email: vraut@clemson.edu<BR>Phone:
864-650-1431<BR>--------------------------------------------------------------------------------------------------------------------------------------------<BR></P></BLOCKQUOTE></BODY></HTML>