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 <[EMAIL PROTECTED]> 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
> <[EMAIL PROTECTED]> 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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