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