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 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 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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