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

[David van der Spoel]

On Tue, 2004-05-25 at 21:59, Yinghong wrote:
> Dear David:
> 
> Thanks very much for your suggestion, I have smoothly cracked the
> problem after modifying "xlateat.dat".
> 
> Another problem, how can I write the terminal database with (-CHOH)?
> and the defined one in rtp file is (-CH-) or (-CHO-).
> 
you mean you want to have a CHOH terminus, instead of COOH?
In that case copy the file XXX-c.tdb to your working directory and add
an entry for CHOH. Note that XXX stands for the force field you are
working with,
>  
> 
> Xie YH
> 
> > 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.
________________________________________________________________________
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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