Dear Amber Users,
Can anybody please suggest that whether I can do eq dynamics for discontinuous residues on pdb file like this:
ATOM 6160 CA VAL V 495
-26.907 27.953 10.881 1.00
0.00 C
ATOM 6161 C VAL V
495 -25.487 27.701 11.433
1.00
0.00 C
ATOM 6162 O VAL V
495 -24.601 27.370 10.645
1.00
0.00 O
ATOM 6163 CB VAL V 495
-27.628 26.633 10.484 1.00
0.00 C
ATOM 6164 CG1 VAL V 495
-29.149 26.835 10.392 1.00
0.00 C
ATOM 6165 CG2 VAL V 495
-27.097 25.950 9.206 1.00
0.00 C
ATOM 6176 N SER S
70 -13.765 51.081 -32.525
1.00
0.00 N
ATOM 6177 CA SER S
70 -14.432 52.362 -32.310
1.00
0.00 C
ATOM 6178 C SER S
70 -15.951 52.230 -32.471
1.00
0.00 C
ATOM 6179 O SER S
70 -16.441 51.635 -33.431
1.00
0.00 O
ATOM 6180 CB SER S
70 -13.908 53.383 -33.338
1.00
0.00 C
ATOM 6181 OG SER S
70 -12.648 53.891 -32.958
1.00
0.00 O
ATOM 6187 N SER S
116 -12.379 71.293 -5.959
1.00
0.00 N
ATOM 6188 CA SER S 116
-13.531 70.836 -5.197 1.00
0.00 C
ATOM 6189 C SER S
116 -14.158 69.663 -5.970
1.00
0.00 C
ATOM 6190 O SER S
116 -15.366 69.618 -6.186
1.00
0.00 O
ATOM 6191 CB SER S 116
-14.495 72.032 -5.065 1.00
0.00 C
ATOM 6192 OG SER S 116
-13.929 73.075 -4.299 1.00
0.00 O
ATOM 6198 N SER S
135 -4.828 59.572
-0.373 1.00
0.00 N
ATOM 6199 CA SER S
135 -5.627 58.388
-0.085 1.00
0.00 C
ATOM 6200 C SER S
135 -4.797 57.096
-0.026 1.00
0.00 C
ATOM 6201 O SER S
135 -4.987 56.337
0.919 1.00
0.00 O
ATOM 6202 CB SER S
135 -6.815 58.284
-1.050 1.00
0.00 C
ATOM 6203 OG SER S
135 -7.801 59.242
-0.716 1.00
0.00 O
here two problems are there:
1) If I dont insert TER between discontinued residue AMBER makes a bond between far residues like 495 and 70
2) If I insert TER between discontinued residues then AMBER considers
and adds missing atom OXT. OXT is not desired as CO is free end.
here no bond id fromed as expected between far residues
3) Also if I remove added OXT atoms then the discontinous residues, as
they are not bonded, will fly away during dynamics and it is not good
to put positional restraints.
So please suggest is it possible to dynamics in this case or I should consider the full sequence....
thanks and regards,
JIomm
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Received on Tue Jun 01 2010 - 00:00:03 PDT
