Hi David,<br> <br> 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. <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 all,<br>> <br>> I am trying to run a gromacs trajectory on a ligand-receptor complex, <br>> where the ligand is a head-to-tail cyclic peptide. I add the -ter option <br>> in the pdb2gmx command, so that i can turn off the charged termini in <br>> the peptide. Unfortunately, it will only work keeping the N terminus as <br>> -NH2 (meaning it will add two hydrogens on the resulting structure) or <br>> as N (in this case it doesn't add any hydrogens). They are both 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 means i <br>> have to change all the remaining atoms, all angles, dihedrals etc. Its <br>> just impossible as my complex has about 3.000 atoms! Any 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>> 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></blockquote><br><p> 
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