How to acetylate at the N terminus and amidate at the C terminus

From: ydhuang2727 (ydhuang2727_at_163.com)
Date: Tue Dec 22 2009 - 21:10:45 CST

Dear all,
 
I'm going to simulate a small peptide extracted from a protein.
The N terminus is acetylated and the C terminus is amidated in the original .pdb file. I guess the main purpose is to shield the C,N terminus.
 
Part of my pdb file is as follows:
HETATM 1 C ACE A 0 -1.837 8.502 -1.974 1.00 1.00 C
HETATM 2 O ACE A 0 -1.385 8.188 -3.074 1.00 1.00 O
HETATM 3 CH3 ACE A 0 -1.233 9.623 -1.200 1.00 1.00 C
HETATM 4 H1 ACE A 0 -0.712 10.296 -1.881 1.00 1.00 H
HETATM 5 H2 ACE A 0 -0.525 9.223 -0.473 1.00 1.00 H
HETATM 6 H3 ACE A 0 -2.018 10.170 -0.679 1.00 1.00 H
ATOM 7 N ASP A 1 -2.863 7.904 -1.386 1.00 1.00 N
ATOM 8 CA ASP A 1 -3.558 6.804 -2.031 1.00 1.00 C
ATOM 9 C ASP A 1 -4.697 7.318 -2.915 1.00 1.00 C
ATOM 10 O ASP A 1 -5.472 8.176 -2.497 1.00 1.00 O
ATOM 11 CB ASP A 1 -4.148 5.957 -0.902 1.00 1.00 C
ATOM 12 CG ASP A 1 -3.118 5.260 -0.011 1.00 1.00 C
ATOM 13 OD1 ASP A 1 -2.722 4.132 -0.377 1.00 1.00 O
ATOM 14 OD2 ASP A 1 -2.749 5.870 1.015 1.00 1.00 O
ATOM 15 H ASP A 1 -3.218 8.160 -0.487 1.00 1.00 H
ATOM 16 HA ASP A 1 -2.839 6.270 -2.652 1.00 1.00 H
ATOM 17 HB2 ASP A 1 -4.773 6.596 -0.278 1.00 1.00 H
ATOM 18 HB3 ASP A 1 -4.800 5.201 -1.338 1.00 1.00 H
.. ...
ATOM 238 N LYS A 16 1.014 6.436 -3.753 1.00 1.00 N
ATOM 239 CA LYS A 16 0.619 5.153 -4.309 1.00 1.00 C
ATOM 240 C LYS A 16 0.930 5.134 -5.806 1.00 1.00 C
ATOM 241 O LYS A 16 0.020 5.096 -6.633 1.00 1.00 O
ATOM 242 CB LYS A 16 -0.846 4.855 -3.981 1.00 1.00 C
ATOM 243 CG LYS A 16 -1.106 3.348 -3.954 1.00 1.00 C
ATOM 244 CD LYS A 16 -0.668 2.739 -2.621 1.00 1.00 C
ATOM 245 CE LYS A 16 -1.432 1.445 -2.331 1.00 1.00 C
ATOM 246 NZ LYS A 16 -2.774 1.747 -1.785 1.00 1.00 N
ATOM 247 H LYS A 16 0.269 7.093 -3.635 1.00 1.00 H
ATOM 248 HA LYS A 16 1.221 4.387 -3.821 1.00 1.00 H
ATOM 249 HB2 LYS A 16 -1.102 5.289 -3.014 1.00 1.00 H
ATOM 250 HB3 LYS A 16 -1.491 5.326 -4.722 1.00 1.00 H
ATOM 251 HG2 LYS A 16 -2.166 3.155 -4.116 1.00 1.00 H
ATOM 252 HG3 LYS A 16 -0.567 2.868 -4.771 1.00 1.00 H
ATOM 253 HD2 LYS A 16 0.402 2.536 -2.643 1.00 1.00 H
ATOM 254 HD3 LYS A 16 -0.840 3.455 -1.816 1.00 1.00 H
ATOM 255 HE2 LYS A 16 -1.528 0.861 -3.246 1.00 1.00 H
ATOM 256 HE3 LYS A 16 -0.872 0.837 -1.621 1.00 1.00 H
ATOM 257 HZ1 LYS A 16 -3.410 1.917 -2.538 1.00 1.00 H
ATOM 258 HZ2 LYS A 16 -3.097 0.969 -1.246 1.00 1.00 H
ATOM 259 HZ3 LYS A 16 -2.723 2.558 -1.203 1.00 1.00 H
HETATM 260 N NH2 A 17 2.220 5.161 -6.111 1.00 1.00 N
HETATM 261 HN1 NH2 A 17 2.512 5.149 -7.082 1.00 1.00 H
HETATM 262 HN2 NH2 A 17 2.914 5.194 -5.373 1.00 1.00 H
TER 263 NH2 A 17

There is PRES ACE for N terminus in the topological file top_all22_prot.inp, but i don't know the corresponding command needed in the input file of the GENPSF program.
 
On the other hand, there is no PRES NH2 for C terminus, how to deal with it?
 
Though, it's generally defaulted that the N-ter is NH3+ and C-ter is COO- rather than neuralized in the psfgen program, i still don't understand the real reason mainly due to my poor biochemistry background. Will anybody analyze the reason for me by the way?
 
Thanks for all your time!
 
 
 
 
All the best,
 
Yandong Huang,
 

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