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  • Ghemical: Molecular modelling - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #261 ] Wrong PDB to MDL conversion on Linux?
    Date:
    05/23/06 09:33
    Submitted by:
    unset
    Assigned to:
    unset
    Category:
    Compilation/Installation
    Priority:
    5
    Ticket group:
    Need to Fix
    Resolution:
    Unset
    Summary:
    Wrong PDB to MDL conversion on Linux?
    Original submission:
    Hello,
    I am having problems in converting PDB files to mdl on Linux. I tried a couple of versions of babel. The main problem is that the type of bond info is different. For example, if I use 1A07.pdb I get all single bonds whereas the windows version as was given to me by someone else gives double as well as tripple bonds. I had the same problem with mol and mol2 formats too.

    I am using Mandriva 2006.0 and Mandrake 10.2 and both give the same problems.

    Output reg bonds from windows version that was given to me:
    1 2 1 0 0 0
    1 7 1 0 0 0
    1 8 1 0 0 0
    1 9 1 0 0 0
    2 3 1 0 0 0
    2 5 1 0 0 0
    3 4 2 0 0 0
    3 11 1 0 0 0
    5 6 1 0 0 0
    6 10 1 0 0 0
    11 12 1 0 0 0
    11 19 1 0 0 0
    12 13 1 0 0 0
    12 15 1 0 0 0


    Output from Linux version:
    M V30 1 1 9 1
    M V30 2 1 8 1
    M V30 3 1 1 7
    M V30 4 1 1 2
    M V30 5 1 2 3
    M V30 6 1 2 5
    M V30 7 1 3 11
    M V30 8 1 3 4
    M V30 9 1 5 6
    M V30 10 1 10 6
    M V30 11 1 19 11
    M V30 12 1 11 12
    M V30 13 1 15 12
    M V30 14 1 12 13


    I am trying to obtain information on all bonds that are present. But I am only getting single bonds from mol, mol2 and mdl formats. I would like to know if this is a bug or if I am going the wrong way.

    Thanks in advance for any help.
    -S

    PS: Usage:

    For mol format (similar for mdl and mol2):
    $ babel -x3 -ipdb 1A07.pdb -omol 1A07.mol
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    Followups
    Comment Date By
    It seems that the problem arises upon the PDB file being large. That is if I cut the PDB son that only a few residues are present, it will work fine, otherwise it doesn't! 05/23/06 10:08 sinedie
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