AMBER Archive (2008)

Subject: AMBER: Calculate the RESP charge Fe3+ of heme (p450)

From: chen bents (bentschen_at_gmail.com)
Date: Thu May 22 2008 - 21:16:12 CDT

Dear all:

            I want to get the RESP charge of heme(p450) , i got that ESP
charge use gaussia03 software.and then use the antechamber programme of
AMBER ,because i want to get the gaff of heme.When i run the command :
antechamber -i cys.mol2 -fi mol2 -o cys.ac -fo ac -c rc -cf qout_stage2
.There was a erro: For atom[1]:Fe1, the best APS is not zero, exit
Info: Bond types are assigned for valence state 7 with penalty of 2. I use
another command try to get the the ac file : antechamber -i cys.out -fi gout
-o cys.ac -fo ac -c resp .the detail of the output file cys.ac below:
ATOM 1 Fe1 MOL 1 0.837 0.028 -0.483 0.000001 Fe
ATOM 2 N1 MOL 1 -0.299 1.381 -1.358 0.000020 nc
ATOM 3 N2 MOL 1 2.056 1.457 0.158 0.000020 nc
ATOM 4 N3 MOL 1 2.184 -1.314 0.086 0.000020 nc
ATOM 5 N4 MOL 1 -0.194 -1.385 -1.394 0.000020 nc
ATOM 6 C1 MOL 1 -1.364 1.185 -2.209 -0.000002 cc
ATOM 7 C2 MOL 1 -0.255 2.742 -1.155 -0.000002 cd
ATOM 8 C3 MOL 1 1.791 2.805 0.176 -0.000002 cc
ATOM 9 C4 MOL 1 3.275 1.328 0.782 -0.000002 cd
ATOM 10 C5 MOL 1 3.389 -1.105 0.715 -0.000002 cc
ATOM 11 C6 MOL 1 2.034 -2.680 0.054 -0.000002 cd
ATOM 12 C7 MOL 1 -0.037 -2.744 -1.238 -0.000002 cc
ATOM 13 C8 MOL 1 -1.272 -1.249 -2.239 -0.000002 cd
ATOM 14 C9 MOL 1 -1.815 -0.046 -2.641 -0.000017 cf
ATOM 15 C10 MOL 1 0.697 3.408 -0.410 -0.000017 cf
ATOM 16 C11 MOL 1 3.916 0.131 1.027 -0.000017 cf
ATOM 17 C12 MOL 1 0.983 -3.353 -0.534 -0.000017 cf
ATOM 18 C13 MOL 1 -1.985 2.435 -2.548 -0.000032 cc
ATOM 19 C14 MOL 1 -1.303 3.400 -1.883 -0.000032 cd
ATOM 20 C15 MOL 1 2.853 3.527 0.821 -0.000032 cc
ATATOM 22 C17 MOL 1 4.010 -2.354 1.061 -0.000032 cc
ATOM 23 C18 MOL 1 3.162 -3.333 0.662 -0.000032 cd
ATOM 24 C19 MOL 1 -1.034 -3.462 -1.982 -0.000032 cc
ATOM 25 C20 MOL 1 -1.793 -2.533 -2.616 -0.000032 cd
ATOM 26 H1 MOL 1 -2.839 2.539 -3.203 -0.000001 ha
ATOM 27 H2 MOL 1 -1.475 4.467 -1.883 -0.000001 ha
ATOM 28 H3 MOL 1 2.875 4.600 0.955 -0.000001 ha
ATOM 29 H4 MOL 1 4.726 2.767 1.689 -0.000001 ha
ATOM 30 H5 MOL 1 4.967 -2.448 1.555 -0.000001 ha
ATOM 31 H6 MOL 1 3.277 -4.404 0.753 -0.000001 ha
ATOM 32 H7 MOL 1 -1.115 -4.539 -2.020 -0.000001 ha
ATOM 33 H8 MOL 1 -2.635 -2.686 -3.277 -0.000001 ha
ATOM 34 H9 MOL 1 0.612 4.486 -0.331 0.000080 ha
ATOM 35 H10 MOL 1 4.876 0.162 1.530 0.000080 ha
ATOM 36 H11 MOL 1 0.990 -4.436 -0.492 0.000080 ha
ATOM 37 H12 MOL 1 -2.671 -0.069 -3.306 0.000080 ha
ATOM 38 S1 MOL 1 -0.215 -0.028 1.404 -0.000031 s
ATOM 39 C21 MOL 1 -1.979 -0.268 1.011 -0.000322 c3
ATOM 40 H13 MOL 1 -2.268 0.340 0.155 0.000302 h1
ATOM 41 H14 MOL 1 -2.162 -1.318 0.756 0.000302 h1
ATOM 42 C22 MOL 1 -2.848 0.133 2.210 0.000011 c3
ATOM 43 H15 MOL 1 -2.622 1.182 2.442 -0.000360 h1

so could any friends tell me the reason , or how to get the gaff file of
heme (p450) ~~~~ thanks in advance~ ~

yours bents

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