From: hem_chandra_at_iitg.ernet.in
Date: Fri Mar 31 2017 - 04:03:15 CDT
Hello Namd,
1. top_all36_rtf contains a residue defined as PRES CT1. I want to patch
this to the last residue of my protein.
2. another molecule BOC (whose cgenff generated str file is attached
herewith), which I want to patch it to the first residue of the peptide
chain.
https://drive.google.com/open?id=0B77lRAKVhq_RZjJXQ0haZlhhRjg
https://drive.google.com/open?id=0B77lRAKVhq_RWWlkTE0zajRTY00
please suggest me how I should do it using NAMD.
Thanking in anticipation
_hem
ps:
### this is just a concerened part from top_all36_prot.rtf
PRES CT1 0.00 ! methylated C-terminus from methyl acetate
GROUP ! use in generate statement
ATOM N NH1 -0.47 ! don't use with Gly or Pro
ATOM HN H 0.31 ! OT1
ATOM CA CT1 0.17 ! | //
ATOM HA HB1 0.09 ! -N--CA--C HT1
ATOM C CD 0.63 ! | | \ /
ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
ATOM OT2 OS -0.34 ! \
ATOM CT CT3 -0.14 ! HT3
ATOM HT1 HA3 0.09 !
ATOM HT2 HA3 0.09 !
ATOM HT3 HA3 0.09 !
DELETE ATOM O
BOND C OT2 OT2 CT
BOND CT HT1 CT HT2 CT HT3
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:11 CST