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<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>Hi,
all,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=052173909-25102006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>I want to simulate a
unit cell of a protein under pbc. The whole system consists of about 100
chains. In original .pdb file, some chain IDs are identical, for example, 'A' is
used for different chains. When I used that file without revision, gmx showed
error like that: Chain identifier 'A' was used in two non-sequential blocks. So
I had to delete all chain ID and hope that gmx can add them automatically
accordint to its rule. Please not that there is "TER" at the end of every
chain in my file. But strangely, gmx did not recognize "TER" and consider some
chains as one and results in some "long bond" warning. So what can I do now?
Bacially, I maybe have two ways:</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=052173909-25102006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>1,
add different chain ID for each one, but I can't find enough
characters to do this;</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>2, make gmx do
some help, but I can not figure out how to do till now.</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=052173909-25102006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>Any suggestions are
welcome</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=052173909-25102006></SPAN></FONT> </DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>Zhongqiao
Hu</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>Dept. of Chemical
and Biomolecular Engineering</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=052173909-25102006>National Univ. of
Singapore</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN
class=052173909-25102006> </SPAN></FONT></DIV>
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