How do I set this up? Looking at the tutorial, I assuming as follows:
1) Leave the original PDB untouched
2) Create a lib file for HIP (as I can't use the one from amber due to
reordering)
3) Move the only atoms that are different between the two after the C and O
atoms, in this case it is the delta protin (HD1).
In the first PDB I have:
ATOM 3920 N HIE 252 27.329 52.218 59.744 1.00
0.00 N
ATOM 3921 H HIE 252 26.567 52.021 59.111 1.00
0.00 H
ATOM 3922 CA HIE 252 27.688 51.188 60.699 1.00
0.00 C
ATOM 3923 HA HIE 252 28.775 51.117 60.665 1.00
0.00 H
ATOM 3924 CB HIE 252 27.031 51.445 62.092 1.00
0.00 C
ATOM 3925 HB2 HIE 252 27.106 52.494 62.377 1.00
0.00 H
ATOM 3926 HB3 HIE 252 25.971 51.206 62.005 1.00
0.00 H
ATOM 3927 CG HIE 252 27.688 50.670 63.233 1.00
0.00 C
ATOM 3928 ND1 HIE 252 29.010 50.292 63.429 1.00
0.00 N
ATOM 3930 CE1 HIE 252 29.103 49.910 64.747 1.00
0.00 C
ATOM 3931 HE1 HIE 252 30.023 49.700 65.273 1.00
0.00 H
ATOM 3932 NE2 HIE 252 27.856 49.834 65.234 1.00
0.00 N
ATOM 3933 HE2 HIE 252 27.688 49.538 66.185 1.00
0.00 H
ATOM 3934 CD2 HIE 252 26.935 50.410 64.358 1.00
0.00 C
ATOM 3935 HD2 HIE 252 25.919 50.739 64.521 1.00
0.00 H
ATOM 3936 C HIE 252 27.342 49.765 60.174 1.00
0.00 C
ATOM 3937 O HIE 252 26.324 49.560 59.539 1.00
0.00 O
In the second PDB I have:
ATOM 3920 N MHP 252 27.329 52.218 59.744 1.00
0.00 N
ATOM 3921 H MHP 252 26.567 52.021 59.111 1.00
0.00 H
ATOM 3922 CA MHP 252 27.688 51.188 60.699 1.00
0.00 C
ATOM 3923 HA MHP 252 28.775 51.117 60.665 1.00
0.00 H
ATOM 3924 CB MHP 252 27.031 51.445 62.092 1.00
0.00 C
ATOM 3925 HB2 MHP 252 27.106 52.494 62.377 1.00
0.00 H
ATOM 3926 HB3 MHP 252 25.971 51.206 62.005 1.00
0.00 H
ATOM 3927 CG MHP 252 27.688 50.670 63.233 1.00
0.00 C
ATOM 3928 ND1 MHP 252 29.010 50.292 63.429 1.00
0.00 N
ATOM 3930 CE1 MHP 252 29.103 49.910 64.747 1.00
0.00 C
ATOM 3931 HE1 MHP 252 30.023 49.700 65.273 1.00
0.00 H
ATOM 3932 NE2 MHP 252 27.856 49.834 65.234 1.00
0.00 N
ATOM 3933 HE2 MHP 252 27.688 49.538 66.185 1.00
0.00 H
ATOM 3934 CD2 MHP 252 26.935 50.410 64.358 1.00
0.00 C
ATOM 3935 HD2 MHP 252 25.919 50.739 64.521 1.00
0.00 H
ATOM 3936 C MHP 252 27.342 49.765 60.174 1.00
0.00 C
ATOM 3937 O MHP 252 26.324 49.560 59.539 1.00
0.00 O
*ATOM 3929 HD1 MHP 252 29.713 50.431 62.718 1.00
0.00 H *
Is there an easy way to generate a lib file of my new HIP residue?
Best Regards,
Drew
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Received on Thu Dec 14 2017 - 10:00:02 PST
