Charles, Thank you for your quick response. I added in the improper parameter as you suggested. This part is working. Now I run into another error message: Some bond angles are missing in the topology and parameter file that involve this donor atom (-C).
We need your advice on this again. Thank you for your help. The following is the topology file I have so far. presidue CTOH ! C-terminal for all, CH2OH at end "* - CTOH" delete atom -O type=O charge=-0.48 end group modify atom -C type=CT charge= 0.08 end add atom -H1 type=HA charge= 0.10 end add atom -H2 type=HA charge= 0.10 end group modify atom -O type=OH charge=-0.68 end add atom -H3 type=H charge= 0.40 end add bond -C -H1 add bond -C -H2 add bond -C -O add bond -O -H3 add angle -CA -C -H1 add angle -CA -C -H2 add angle -H1 -C -O add angle -H2 -C -O add angle -C -O -H3 add angle -HA -CA -C add angle -CB -CA -C add angle -N -CA -C add improper H1 H2 CA O !stereo CH2 add dihedral O C CA CB end Lixin mal at health.missouri.edu -----Original Message----- From: Charles at Schwieters.org [mailto:[email protected]] Sent: Friday, December 21, 2007 3:15 PM To: Ma, Lixin Cc: xplor-nih at nmr.cit.nih.gov; Dannoon, Shorouk Faleh (UMC-Student) Subject: Re: [Xplor-nih] adding alcohol C-terminal capping -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Lixin-- > We have trouble adding C-terminal CH2OH group on the last residue Thr. > We made a presidue CTOH as following. However it didn't work, we had > error msgs such as missing improper parameters, improper energy > constant missing, target improper value missing. What did we miss in > this topology file? or do we have another way to get the c terminal > capped on? You changed the type of the C atom, so so need to specify a new improper parameter: param improper HA NH1 CT CT $kchi 0 65.977 ! CA chirality end ok? Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFHbCzOPK2zrJwS/lYRAljJAJ92HSrXUPxQQ4OE7vuXRGYD2iJKUwCfV/vm lPOtcFAKs8J6aOVqt/XJzc4= =5Jdm -----END PGP SIGNATURE-----
