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

[David]

On Tue, 2004-05-25 at 01:15, Yinghong wrote:
> 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.
try 
pdb2gmx -ter 
and select none for both termini.

> 
> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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