<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=gb2312">
<META content="MSHTML 6.00.2800.1106" name=GENERATOR></HEAD>
<BODY>
<P>Dear gmx users:</P>
<P>While simulating DNA molecules via Gromacs, a fatal error always happened,
that is "Residue xxx not found in the residue topology database".</P>
<P>Actually, I know that the residue name in the .pdb file must be the same as
ff***.rtp, so I modified these files by 'sed' command, either</P>
<P>Just changing the A C G T residues in the original pdb file to DADE, DCYT,
DGUA, DTHY, and the latter is the same as those in ff***.rtp
files;</P>
<P>or</P>
<P>Only changing the DADE, DCYT, DGUA, DTHY in the ff***.rtp to A C G
T as presented in the pdb files.</P>
<P>Anyway, the purpose of these modifications is to make residue names
be the same between pdb and ff***.rtp files. However, all of
these could not yet work well, and the error "Residue xxx not
found in the residue topology database" is still emerged.</P>
<P>Therefore, I am now quite confused, and also hope your help!</P>
<P> </P>
<P>Thanks in advance.</P>
<P> </P>
<P>Yours,</P>
<P>Xie YH</P>
<P>The University of Hongkong</P></BODY></HTML>