[AMBER] Problem related to the load PDB

From: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Date: Wed, 15 Jun 2011 11:27:18 +0530 (IST)

Hello!


I have a crystal structure of an enzyme (HisRS) which is tetramer. The residues between 185 to 228 are missing for all chains. How to manage this issue?

If I load the pdb file as it is then it forms a bond between the residue 185 and 228 which is unnatural. A part of the pdb file showing the coordinate of residue 185 and residue 228 is shown as follows:
  
ATOM   1793  N   LEU A 185       2.488  44.813   7.408  1.00 77.39           N 
ATOM   1794  CA  LEU A 185       3.537  43.802   7.492  1.00 80.42           C 
ATOM   1795  C   LEU A 185       4.779  44.212   6.665  1.00 82.35           C 
ATOM   1796  O   LEU A 185       5.855  44.529   7.215  1.00 83.14           O 
ATOM   1797  CB  LEU A 185       2.993  42.429   7.043  1.00 79.48           C 
ATOM   1798  H   LEU A 185       1.645  44.592   6.981  1.00  0.00           H 
ATOM   1799  N   TYR A 228     -12.077  46.733  12.305  1.00 60.84           N 
ATOM   1800  CA  TYR A 228     -12.163  46.419  10.872  1.00 61.23           C 
ATOM   1801  C   TYR A 228     -13.202  45.304  10.589  1.00 61.67           C 
ATOM   1802  O   TYR A 228     -13.126  44.609   9.561  1.00 61.76           O 
ATOM   1803  CB  TYR A 228     -10.757  46.026  10.324  1.00 60.27           C 
ATOM   1804  H   TYR A 228     -12.893  46.851  12.828  1.00  0.00           H 
 
If I add ‘TER’ in between the coordinates of residue 185 and coordinate of residue 228 then leap consider the 185 residue as C-terminal residue and 228 residue as N-terminal residue and creates one additional positive charge for the amino croup of 185 residue and a negative charge for the carboxylic acid group of 228 residue. A part of the pdb file showing the coordinate of residue 185 and residue 228 in the modified pdb file is shown as follows:

ATOM   1793  N   LEU A 185       2.488  44.813   7.408  1.00 77.39           N 
ATOM   1794  CA  LEU A 185       3.537  43.802   7.492  1.00 80.42           C 
ATOM   1795  C   LEU A 185       4.779  44.212   6.665  1.00 82.35           C 
ATOM   1796  O   LEU A 185       5.855  44.529   7.215  1.00 83.14           O 
ATOM   1797  CB  LEU A 185       2.993  42.429   7.043  1.00 79.48           C 
ATOM   1798  H   LEU A 185       1.645  44.592   6.981  1.00  0.00           H
TER
ATOM   1799  N   TYR A 228     -12.077  46.733  12.305  1.00 60.84           N 
ATOM   1800  CA  TYR A 228     -12.163  46.419  10.872  1.00 61.23           C 
ATOM   1801  C   TYR A 228     -13.202  45.304  10.589  1.00 61.67           C 
ATOM   1802  O   TYR A 228     -13.126  44.609   9.561  1.00 61.76           O 
ATOM   1803  CB  TYR A 228     -10.757  46.026  10.324  1.00 60.27           C 
 
Now I want to make the carboxylic acid group (-COO-) of 185 residue and amino group of (-NH3+) residue 228 as neutral. How to do this? I also want to know in general what is used in such cases.  
  
With best regards
Sindrila   
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Received on Tue Jun 14 2011 - 23:00:05 PDT
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