(unknown charset) [AMBER] ANAL

From: (unknown charset) 王伟 <ww5945.163.com>
Date: Sun, 25 Mar 2012 11:17:43 +0800 (CST)

Sir I have been using AMBER9 on RED HAT Linux. Recently,I want to perform the ANAL module of Amber9 to assess the contributions of different structural moieties of the inhibitor to the interaction energy of the inhibitor with the protein. But in the ANAL input file,I can not correctly define the group format of the inhibitor. so here I want to know how I will write it. I have read the section on GROUP in the Appendices, and there is an example of The molecule 18-crown-6 in it, I just can not understand how he created three new residues in the PREP unit. because my system is a protein-ligand complex and in its pdb file, my ligand is regarded as residue 443, my pdb file is like below:

.........
ATOM 3556 O GLY 442 42.694 -35.011 90.484 0.00 0.00 O
ATOM 3557 OXT GLY 442 41.583 -36.809 90.977 0.00 0.00 O
TER 3558 GLY 442
HETATM 3559 C1 MOL 443 43.908 14.787 98.515 0.00 0.00 C
HETATM 3560 S2 MOL 443 43.597 15.718 99.982 0.00 0.00 S
HETATM 3561 C3 MOL 443 43.701 17.085 98.846 0.00 0.00 C
HETATM 3562 N4 MOL 443 43.788 16.851 97.566 0.00 0.00 N
HETATM 3563 C5 MOL 443 43.858 15.522 97.350 0.00 0.00 C
HETATM 3564 N6 MOL 443 43.502 18.351 99.315 0.00 0.00 N1+
HETATM 3565 C7 MOL 443 43.195 18.710 100.523 0.00 0.00 C
HETATM 3566 O8 MOL 443 43.563 18.103 101.534 0.00 0.00 O
HETATM 3567 C9 MOL 443 44.155 13.310 98.533 0.00 0.00 C
HETATM 3568 C10 MOL 443 45.504 13.072 99.258 0.00 0.00 C
HETATM 3569 C11 MOL 443 42.908 12.606 99.055 0.00 0.00 C
HETATM 3570 C21 MOL 443 42.574 20.089 100.731 0.00 0.00 C
HETATM 3571 C22 MOL 443 43.407 20.881 101.694 0.00 0.00 C
HETATM 3572 C23 MOL 443 44.025 22.069 101.363 0.00 0.00 C
HETATM 3573 C24 MOL 443 44.715 22.865 102.306 0.00 0.00 C
HETATM 3574 C25 MOL 443 44.695 22.429 103.640 0.00 0.00 C
HETATM 3575 C26 MOL 443 43.997 21.306 104.057 0.00 0.00 C
HETATM 3576 C27 MOL 443 43.366 20.534 103.072 0.00 0.00 C
TER 3577 MOL 443
END

then I just write my anal input-file like this :

Analysis of complex
1 0 0 0 70 1
0 0.0 0.0 0.0 0.0
1 0.0 0.0 0.0 0.0 0
99.0 2.0 1.2 1
1 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
ENERGY
test_1
Atom 3559 3563
END
test_2
Atom 3564 3566
END
test_3
Atom 3567 3569
END
test_4
Atom 3570 3577
END
END
STOPand It will soon terminate with errorsHere I intend to devide the ligand into four groups, and then assess the contributions of different structural groups of the inhibitor to the interaction energy of the inhibitor with the protein. so I want to get your help. Thanks

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Received on Sat Mar 24 2012 - 20:30:02 PDT
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