[gmx-users] cyclic peptides

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 17 13:13:02 CEST 2006

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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