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<DIV><FONT face=Arial size=2>Try renaming CYX to CYS, pdb2gmx should find the
disulfide bond by itself.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>marc</FONT></DIV>
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<DIV style="FONT: 10pt arial">----- Original Message ----- </DIV>
<DIV
style="BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: black"><B>From:</B>
<A title=PNAGY@UTNet.UToledo.Edu href="mailto:PNAGY@UTNet.UToledo.Edu">Nagy,
Peter I.</A> </DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=gmx-users@gromacs.org
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Friday, August 01, 2003 7:51
PM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> [gmx-users] disulfide bond</DIV>
<DIV><BR></DIV><!-- Converted from text/plain format -->
<P><FONT size=2>Dear Gromacs Users!<BR><BR> I created a pdb file
for a protein in Sybyl, where I had a disulfide bond.<BR>Sybyl distinguished
these two residues by CYX as compared to the regular CYS.<BR> When
I used pdb2gmx, the system complained about CYX and responded that<BR>tries to
consider these residues as CYS2. It was fine, but in the conf.gro and
topol.top files I noticed that the backbone H (to N) was not
generated.<BR>Furthermore, the S-S bond was not generated in the topol.top
file.<BR> Perhaps I could edit this latter file by following the
topology and charge<BR>parameters for a backbone H(N), but I do not have its
coordinates in the conf.gro. I am sure that there is a simple way to handle
the S-S in Gromacs.<BR> What should I modify in the original .pdf
file to get correct .gro and<BR>.top files?<BR><BR>Thanks, Peter
Nagy<BR>pnagy@utnet.utoledo.edu</FONT> </P></BLOCKQUOTE></BODY></HTML>