From: Vidhya Sankar (vidhyasankar7928_at_yahoo.com)
Date: Sun Nov 03 2013 - 00:08:11 CDT
Dear Namd users Thank you for your previous reply
I am trying to create psfgen for my cyclicpeptide (having 1 to 14 Residue)
I have searched the mailing List and got previous discussion as in the following hyper link
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22439.html
I have followed that But when i patch the First residue (ARG) and Last residue (PRO)
Using the following commands
patch LINK U:14 U:1
I have got error as follows
no atom O in residue PRO:14 of segment U
Warning: add improper failed in patch LINK
no atom HN in residue ARG:1 of segment U
Warning: add improper failed in patch LINK
no atom HN in residue ARG:1 of segment U
Warning: add conformation failed in patch LINK
no atom O in residue PRO:14 of segment U
Warning: add conformation failed in patch LINK
ARG Residue in my pdb files does not have any NH atom But Topology (top_all36_prot.rtf) has NH atom
Which file Should I edit ? either .rtf or .pdb file to get Compatibility
Thanks in Advance
Withe Regards
S.Vidhyasankar
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