Thank you for reply. Amber force fields have parameters for C-terminal-C(O)-NH2 . But I don't know which of the force fields in Gromacs 3.3.1 have parametrs for the C-terminal amide cap. Is it possible to introduce these parameters manually. What I need to know is that which other files do I need to modify ? Till now I have only modified the terminal database ,( though I may have made some mistake ), but the added "N" 's coordinates are given by pdb2gmx as " nan nan nan"
Thanks in advance Sarbani On Mon, 10 Nov 2008 Mark Abraham wrote : >sarbani chattopadhyay wrote: >> Hi, >> I want to add -NH2 to the c terminal end of my peptide. If I modify the >> " C-terminal >>databse"-> "-c.tdb" , will it be possible to add -NH2 to the "CO" end of the >>last residue at the >>C terminal end. > >For some forcefields, yes. You need the forcefield to have parameters for >(C-terminal) -C (O)-NH2. Not all of them do. Probably the ones that have it parameterized already have the terminus topologies in the database. > >Mark >_______________________________________________ >gmx-users mailing list gmx-users@gromacs.org >http://www.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at http://www.gromacs.org/search before posting! >Please don't post (un)subscribe requests to the list. Use the www interface or >send it to [EMAIL PROTECTED] >Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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