[Xplor-nih] adding alcohol C-terminal capping

[Ma, Lixin]

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:Charles at Schwieters.org] 
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 

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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
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