[gmx-users] David, pls help me with "pdb2gmx"

[Yinghong]

Dear all:
This problem is related to the simulation of sugar (carbohydrate). When executing "pdb2gmx" command, the fatal error as ""Atom O in residue AGC 1 not found in rtp entry with 14 atoms while sorting atoms." happened.
My 'pdb' file is downloaded from website, and I myself defined the corresponding rtp part in the 'ffgmx.rtp' file. Both of them are just as the follows:
=================***.pdb================================
(Assuming this whole structure contains only one AGC residue)
ATOM      1  C1  AGC     1       1.803  -0.843   0.163  0.00  0.00  C1 
ATOM      2  C2  AGC     1       1.161  -0.633   1.531  0.00  0.00  C2 
ATOM      3  C3  AGC     1      -0.346  -0.827   1.489  0.00  0.00  C3 
ATOM      4  C4  AGC     1      -0.954  -0.008   0.373  0.00  0.00  C4 
ATOM      5  C5  AGC     1      -0.250  -0.325  -0.946  0.00  0.00  C5 
ATOM      6  C6  AGC     1      -0.755   0.452  -2.142  0.00  0.00  C6 
ATOM      7  O2  AGC     1       1.739  -1.554   2.447  0.00  0.00 OH2 
ATOM      8  O3  AGC     1      -0.898  -0.399   2.740  0.00  0.00 OH3 
ATOM      9  O5  AGC     1       1.141   0.002  -0.787  0.00  0.00 O10 
ATOM     10 O6  AGC     1      -0.625   1.853  -1.957  0.00  0.00 OH6 
ATOM     11 O1  AGC     1       1.763  -2.177  -0.328  0.00  0.00 OH1 
==========================================================
#############residue topology parameter(within ffgmx.rtp)###################
[ AGC ]                                     
 [ atoms ]
    C1   CS1   0.400     0
    O1    OA  -0.548     0
    O5    OS  -0.360     1
    C5   CS1   0.160     1
    C6   CS2   0.150     2
    O6    OA  -0.548     2
    H6    HO   0.398     2
    C2   CS1   0.150     3
    O2    OA  -0.548     3
    H2    HO   0.398     3
    C3   CS1   0.150     4
    O3    OA  -0.548     4
    H3    HO   0.398     4
    C4   CS1   0.160     5
 [ bonds ]
..
..
..
#################################################################
In the rtp file, three hydrogens H2, H3, H6 are added, which are all the hydrogens in the "-OH". And, the "aminoacid.dat" & "ffgmx.hdb" files are also being modified.
I have tried lots of ways, however, this problem can not yet be solved. 
Waiting for your precious suggestion!
Thanks in advance!


Xie YH
HongKong University
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