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