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<P>Dear David:</P>
<P>As you said, I tried again with "pdb2gmx -ter ...", </P>
<P>however, I have no chance to select none for termini while executing this
command, </P>
<P>and directly encountered the error <EM>"</EM>Atom O in residue AGC 1 not
found in rtp entry with 14 atoms while sorting atoms." </P>
<P> </P>
<P>In my case, the molecule is carbohydrate instead of protein. So there is
no corresponding termini definition in "***.tdb" file at all.</P>
<P>Therefore, as I considered, the problem is not related to termini, maybe
other reasons are existed. What are they?</P>
<P>Can you give me more suggestion?</P>
<P>Thank a lot!</P>
<P> </P>
<P>Xie YH</P>
<P>Hongkong Univ.</P>
<P> </P>
<P>On Tue, 2004-05-25 at 01:15, Yinghong wrote:<BR>><I> Dear
all:<BR></I>><I> <BR></I>><I> This problem is related to the simulation of
sugar (carbohydrate).<BR></I>><I> When executing "pdb2gmx" command, the fatal
error as ""Atom O in<BR></I>><I> residue AGC 1 not found in rtp entry with 14
atoms while sorting<BR></I>><I> atoms." happened.<BR></I>try <BR>pdb2gmx -ter
<BR>and select none for both termini.<BR><BR>><I> <BR></I>><I> My 'pdb'
file is downloaded from website, and I myself defined the<BR></I>><I>
corresponding rtp part in the 'ffgmx.rtp' file. Both of them are
just<BR></I>><I> as the follows:<BR></I>><I> <BR></I>><I>
=================***.pdb================================<BR></I>><I>
<BR></I>><I> (Assuming this whole structure contains only one AGC
residue)<BR></I>><I> <BR></I>><I> ATOM 1 C1 AGC 1 1.803
-0.843 0.163 0.00 0.00 C1</I>><I> ATOM
2 C2 AGC
1 1.161 -0.633 1.531
0.00 0.00 C2<BR></I>><I> ATOM
3 C3 AGC 1
-0.346 -0.827 1.489 0.00 0.00
C3<BR></I>><I> ATOM 4 C4
AGC 1 -0.954
-0.008 0.373 0.00 0.00 C4<BR></I>><I>
ATOM 5 C5 AGC
1 -0.250 -0.325 -0.946
0.00 0.00 C5<BR></I>><I> ATOM
6 C6 AGC 1
-0.755 0.452 -2.142 0.00 0.00
C6<BR></I>><I> ATOM 7 O2
AGC 1 1.739
-1.554 2.447 0.00 0.00 OH2<BR></I>><I>
ATOM 8 O3 AGC
1 -0.898 -0.399 2.740
0.00 0.00 OH3<BR></I>><I> ATOM 9
O5 AGC 1
1.141 0.002 -0.787 0.00 0.00 O10<BR></I>><I>
ATOM 10 O6 AGC
1 -0.625 1.853 -1.957
0.00 0.00 OH6 <BR></I>><I> ATOM 11 O1
AGC 1 1.763
-2.177 -0.328 0.00 0.00 OH1 <BR></I>><I> <BR></I>><I>
==========================================================<BR></I>><I>
<BR></I>><I> #############residue topology parameter(within<BR></I>><I>
ffgmx.rtp)###################<BR></I>><I> <BR></I>><I> [ AGC
]
<BR></I>><I> <BR></I>><I> [ atoms
]<BR></I>><I> C1 CS1
0.400 0<BR></I>><I>
O1 OA -0.548
0<BR></I>><I> O5 OS
-0.360 1<BR></I>><I>
C5 CS1 0.160
1<BR></I>><I> C6 CS2
0.150 2<BR></I>><I>
O6 OA -0.548
2<BR></I>><I> H6 HO
0.398 2<BR></I>><I>
C2 CS1 0.150
3<BR></I>><I> O2 OA
-0.548 3<BR></I>><I>
H2 HO 0.398
3<BR></I>><I> C3 CS1
0.150 4<BR></I>><I>
O3 OA -0.548
4<BR></I>><I> H3 HO
0.398 4<BR></I>><I>
C4 CS1 0.160 5<BR></I>><I>
<BR></I>><I> [ bonds ]<BR></I>><I> ...<BR></I>><I>
<BR></I>><I> ...<BR></I>><I> <BR></I>><I> ...<BR></I>><I>
<BR></I>><I>
#################################################################<BR></I>><I>
<BR></I>><I> In the rtp file, three hydrogens H2, H3, H6 are added, which are
all<BR></I>><I> the hydrogens in the "-OH". And, the "aminoacid.dat" &
"ffgmx.hdb"<BR></I>><I> files are also being modified.<BR></I>><I>
<BR></I>><I> I have tried lots of ways, however, this problem can not yet
be<BR></I>><I> solved. <BR></I>><I> <BR></I>><I> Waiting for your
precious suggestion!<BR></I>><I> <BR></I>><I> Thanks in
advance!<BR></I>><I> <BR></I>><I> <BR></I>><I>
<BR></I>><I> <BR></I>><I> <BR></I>><I> Xie YH<BR></I>><I>
<BR></I>><I> HongKong University<BR></I>><I> <BR></I>><I>
<BR></I>><I> <BR></I>><I> <BR></I>><I> <BR></I>><I>
<BR></I>><I> <BR></I>><I> <BR></I>><I> <BR></I>><I>
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<BR>David.<BR>________________________________________________________________________</P></BODY></HTML>