Efi Mantzourani wrote:
Hi David,

had a look for the specbond entry, but apparently it is for creating a bond between ligand and receptor. I don't have that. Mine is not a special bond. it is just that pdb2gmx tries to find a terminus for all the chains.

just try it anyway. you may have to sepcify the specific residue type of the N-terminus and C-terminus.


*/David van der Spoel <[EMAIL PROTECTED]>/* έγραψε:

    Efi Mantzourani wrote:
     > Hi all,
     >
     > I am trying to run a gromacs trajectory on a ligand-receptor
    complex,
     > where the ligand is a head-to-tail cyclic peptide. I add the -ter
    option
     > in the pdb2gmx command, so that i can turn off the charged
    termini in
     > the peptide. Unfortunately, it will only work keeping the N
    terminus as
     > -NH2 (meaning it will add two hydrogens on the resulting
    structure) or
     > as N (in this case it doesn't add any hydrogens). They are both
    wrong,
     > as I want one hydrogen, like in a normal peptide bond. If i try to
     > change the resulting files manually its a pain! The gro file is easy
     > enough, but the topology file has to be altered so that the added
     > hydrogen is in the correct atom and residue serial number. That
    means i
     > have to change all the remaining atoms, all angles, dihedrals
    etc. Its
     > just impossible as my complex has about 3.000 atoms! Any
    suggestions???

    try making a specbond entry, you have to make sure that the coordinates
    are OK. please report back if succesfull.
     >
     >
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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
    [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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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
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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