[gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

parichita parichita parichitamajumdar at yahoo.co.in
Mon Sep 17 12:20:35 CEST 2007


Hi again.....
  Thank you for your help....
 I found my MANA in the ffG53a5.rtp and i can prepare
the .gro and .top file from pdb2gmx.
Now , i am facing another problem after solvation of
my solute when i run the minimization the 1-6 linkage
was broken ......
please help me out ........
 thanks in advance!
                   parichita.....





--- TJ Piggot <t.piggot at bristol.ac.uk> wrote:

> Just a quick look at the ffG45a3.rtp shows that
> there is an entry for ADE, 
> however the ADE entry is for Adenine.
> 
> For help with your problem check out:
> 
>
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
> 
> Tom
> 
> --On Friday, September 14, 2007 14:13:55 +0100
> parichita parichita 
> <parichitamajumdar at yahoo.co.in> wrote:
> 
> > Hi,
> >
> >      I have facing some problem when converting
> .pdb file to .gro and
> > .top .
> >  I have a .pdb of alpha d-mannose (1-6) alpha
> d-mannose. I was using the
> > pdb2gmx command and 45a3 forcefield .
> >  Showing the fatal error:
> >  Atom O in residue ADE 1 not found in rtp entry
> with 25 atoms
> >               while sorting atoms
> >  and
> > Warning: 'ADMA' not found in residue topology
> database, trying to use
> > 'ADE'
> >  Warning: 'ADMA' not found in residue topology
> database, trying to use
> > 'ADE
> >
> >
> > but in  ffG45a3.rtp I could not found any ADE
> ...........
> >  so I was confused ...
> >  Please give me some suggession.
> >  The format of my M6M.pdb is,
> >
> > ATOM      1  C5  ADMA    1       3.337   1.774 
> -8.944  1.00  0.00
> > C
> >  ATOM      2  O   ADMA    1       4.702   1.679 
> -8.463  1.00  0.00
> > O
> >  ATOM      3  C1  ADMA    1       5.227   0.338 
> -8.248  1.00  0.00
> > C
> >  ATOM      4  C2  ADMA    1       4.345  -0.412 
> -7.222  1.00  0.00
> > C
> >  ATOM      5  O2  ADMA    1       4.481   0.211 
> -5.965  1.00  0.00
> > O
> >  ATOM      6  C3  ADMA    1       2.854  -0.372 
> -7.633  1.00  0.00
> > C
> >  ATOM      7  O3  ADMA    1       2.063  -0.925 
> -6.611  1.00  0.00
> > O
> >  ATOM      8  C4  ADMA    1       2.367   1.065 
> -7.950  1.00  0.00
> > C
> >  ATOM      9  O4  ADMA    1       1.062   1.009 
> -8.476  1.00  0.00
> > O
> >  ATOM     10  C6  ADMA    1       3.018   3.281 
> -9.160  1.00  0.00
> > C
> >  ATOM     11  O6  ADMA    1       1.778   3.456 
> -9.811  1.00  0.00
> > O
> >  ATOM     12  H5  ADMA    1       3.271   1.274 
> -9.929  1.00  0.00
> > H
> >  ATOM     13  H1  ADMA    1       6.262   0.415 
> -7.876  1.00  0.00
> > H
> >  ATOM     14  H2  ADMA    1       4.685  -1.464 
> -7.133  1.00  0.00
> > H
> >  ATOM     15  HO2 ADMA    1       5.425   0.166 
> -5.725  1.00  0.00
> > H
> >  ATOM     16  H3  ADMA    1       2.727  -0.987 
> -8.546  1.00  0.00
> > H
> >  ATOM     17  HO3 ADMA    1       1.139  -0.907 
> -6.925  1.00  0.00
> > H
> >  ATOM     18  H4  ADMA    1       2.343   1.645 
> -7.006  1.00  0.00
> > H
> >  ATOM     19  HO4 ADMA    1       0.779   1.926 
> -8.640  1.00  0.00
> > H
> >  ATOM     20 1H6  ADMA    1       3.805   3.735 
> -9.772  1.00  0.00
> > H
> >  ATOM     21 2H6  ADMA    1       3.014   3.809 
> -8.202  1.00  0.00
> > H
> >  ATOM     22  H6  ADMA    1       1.654   4.401 
> -9.918  1.00  0.00
> > H
> >  ATOM     23  C5  ADMA    1B      5.806  -2.519
> -10.516  1.00  0.00
> > C
> >  ATOM     24  O   ADMA    1B      6.529  -3.735
> -10.196  1.00  0.00
> > O
> >  ATOM     25  C1  ADMA    1B      6.753  -4.668
> -11.291  1.00  0.00
> > C
> >  ATOM     26  O1  ADMA    1B      7.522  -4.046
> -12.268  1.00  0.00
> > O
> >  ATOM     27  C2  ADMA    1B      5.398  -5.107
> -11.893  1.00  0.00
> > C
> >  ATOM     28  O2  ADMA    1B      4.700  -5.870
> -10.935  1.00  0.00
> > O
> >  ATOM     29  C3  ADMA    1B      4.533  -3.881
> -12.271  1.00  0.00
> > C
> >  ATOM     30  O3  ADMA    1B      3.254  -4.305
> -12.671  1.00  0.00
> > O
> >  ATOM     31  C4  ADMA    1B      4.406  -2.866
> -11.106  1.00  0.00
> > C
> >  ATOM     32  O4  ADMA    1B      3.754  -1.706
> -11.569  1.00  0.00
> > O
> >  ATOM     33  C6  ADMA    1B      5.743  -1.655 
> -9.224  1.00  0.00
> > C
> >  ATOM     34  O6  ADMA    1B      5.227  -0.368 
> -9.490  1.00  0.00
> > O
> >  ATOM     35  H5  ADMA    1B      6.383  -1.951
> -11.270  1.00  0.00
> > H
> >  ATOM     36  H1  ADMA    1B      7.300  -5.545
> -10.905  1.00  0.00
> > H
> >  ATOM     37  HO1 ADMA    1B      7.013  -3.281
> -12.602  1.00  0.00
> > H
> >  ATOM     38  H2  ADMA    1B      5.572  -5.738
> -12.788  1.00  0.00
> > H
> >  ATOM     39  HO2 ADMA    1B      5.261  -6.638
> -10.719  1.00  0.00
> > H
> >  ATOM     40  H3  ADMA    1B      5.014  -3.365
> -13.126  1.00  0.00
> > H
> >  ATOM     41  HO3 ADMA    1B      2.756  -3.507
> -12.928  1.00  0.00
> > H
> >  ATOM     42  H4  ADMA    1B      3.788  -3.323
> -10.307  1.00  0.00
> > H
> >  ATOM     43  HO4 ADMA    1B      3.668  -1.103
> -10.809  1.00  0.00
> > H
> >  ATOM     44 1H6  ADMA    1B      6.749  -1.553 
> -8.805  1.00  0.00
> > H
> >  ATOM     45 2H6  ADMA    1B      5.131  -2.153 
> -8.466  1.00  0.00
> > H
> >  TER
> >
> >
> > thanks in advance ..............
> >
> > parichita...........
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Parichita Mazumder
> > Junior Research Fellow
> > C/O Dr. Chaitali Mukhopadhayay
> > Department of Chemistry
> > University of Calcutta
> > 92,A P C Road
> > Kolkata-700009
> > India.
> >
> >
> 
=== message truncated ===


Parichita Mazumder 
Junior Research Fellow 
C/O Dr. Chaitali Mukhopadhayay 
Department of Chemistry 
University of Calcutta 
92,A P C Road 
Kolkata-700009 
India.




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