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

[David]

On Tue, 2004-05-25 at 03:19, Yinghong wrote:
> Dear David:
> 
> As you said, I tried again with "pdb2gmx -ter ...", 
> 
> however, I have no chance to select none for termini while executing
> this command, 
> 
> and directly encountered the error "Atom O in residue AGC 1 not found
> in rtp entry with 14 atoms while sorting atoms." 
> 
>  
> 
> In my case, the molecule is carbohydrate instead of protein. So there
> is no corresponding termini definition in "***.tdb" file at all.
> 
> Therefore, as I considered, the problem is not related to termini,
> maybe other reasons are existed. What are they?
> 
> Can you give me more suggestion?

it could be that the atom name is changed (which is necessary for
proteins).
Copy the file xlateat.dat to your working directory and remove the
entries for O1 and O2
> 
> Thank a lot!
> 
>  
> 
> Xie YH
> 
> Hongkong Univ.
> 
>  
> 
> 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.
> ________________________________________________________________________
> 
> 
> 
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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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