Ok, tried the specbond. That doesn't work on its own. So I changed the forcefield N-terminus database (*.tdb) to give me an extra option for the terminus, [NH]. It seems to work fine, places the hydrogen in the peptide bond, but doesn't know anything about bond angles and dihedrals containing the new atom, fair enough. I then went to the *.itp file of that chain, and filled in the data missing (around 7-8, easy enough). And it seems to work know!<br><br><b><i>David van der Spoel <spoel@xray.bmc.uu.se></i></b> έγραψε:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Efi Mantzourani wrote:<br>> Hi David,<br>> <br>> had a look for the specbond entry, but apparently it is for creating a <br>> bond between ligand and receptor. I don't have that. Mine is not a <br>> special bond. it is just that pdb2gmx tries to find a terminus for all <br>> the chains.<br><br>just try it anyway. you may have
to sepcify the specific residue type of <br>the N-terminus and C-terminus.<br><br>> <br>> */David van der Spoel <spoel@xray.bmc.uu.se>/* έγραψε:<br>> <br>> Efi Mantzourani wrote:<br>> > Hi all,<br>> ><br>> > I am trying to run a gromacs trajectory on a ligand-receptor<br>> complex,<br>> > where the ligand is a head-to-tail cyclic peptide. I add the -ter<br>> option<br>> > in the pdb2gmx command, so that i can turn off the charged<br>> termini in<br>> > the peptide. Unfortunately, it will only work keeping the N<br>> terminus as<br>> > -NH2 (meaning it will add two hydrogens on the resulting<br>> structure) or<br>> > as N (in this case it doesn't add any hydrogens). They are both<br>> wrong,<br>> > as I want one hydrogen, like in a normal peptide bond. If i try to<br>> > change the resulting files manually
its a pain! The gro file is easy<br>> > enough, but the topology file has to be altered so that the added<br>> > hydrogen is in the correct atom and residue serial number. That<br>> means i<br>> > have to change all the remaining atoms, all angles, dihedrals<br>> etc. Its<br>> > just impossible as my complex has about 3.000 atoms! Any<br>> suggestions???<br>> <br>> try making a specbond entry, you have to make sure that the coordinates<br>> are OK. please report back if succesfull.<br>> ><br>> ><br>> ------------------------------------------------------------------------<br>> > Χρησιμοποιείτε Yahoo!<br>> > Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail<br>> διαθέτει την<br>> > καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων<br>> > http://login.yahoo.com/config/mail?.intl=gr<br>>
><br>> ><br>> ><br>> ------------------------------------------------------------------------<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David.<br>> ________________________________________________________________________<br>> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>> Dept. of Cell and Molecular Biology, Uppsala University.<br>> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>> phone: 46 18 471 4205 fax: 46 18 511 755<br>>
spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> ------------------------------------------------------------------------<br>> Χρησιμοποιείτε Yahoo!<br>> Βαρεθήκατε τα ενοχλητικά μηνύ ματα (spam); Το Yahoo! Mail διαθέτει την <br>> καλύτερη δυνατή προστασία κατά των ενοχλητικών μηνυμάτων<br>> http://login.yahoo.com/config/mail?.intl=gr<br>> <br>> <br>> ------------------------------------------------------------------------<br>>
<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list
gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></spoel@xray.bmc.uu.se></blockquote><br><p> 
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