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top_imid.inp
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* CHARMM27 Custom Topology File
* Heme for Cytochrome c
* Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten; last update 12/19/2005
* Classical force field parameters for the heme prosthetic group of cytochrome c.
* Journal of Computational Chemistry, 25, 1613-1622 (2004)
* Journal of Physical Chemistry B, 108, 20376-20387 (2004)
*
31 1
RESI IMD 0.00 ! imidazole
!GROUP
!ATOM N NH1 -0.47 ! HN1 H2
!ATOM HN H 0.31 ! | /
!ATOM CA CT1 0.07 ! N1---C2
!ATOM HA HB 0.09 ! / ||
GROUP ! ! H5--C5 ||
ATOM H5 HR3 -0.09 ! ! \\ ||
!ATOM HB1 HA 0.09 ! C4----N3
!ATOM HB2 HA 0.09 ! |
ATOM N1 NR1 -0.36 ! ! H4
ATOM HN1 H 0.13
ATOM C5 CPH1 -0.05 ! maybe should be CPH1, but shouldn't kill us...
GROUP
ATOM C2 CPH2 0.25
ATOM H2 HR1 0.13
ATOM N3 NR2 -0.70
ATOM C4 CPH1 0.22
ATOM H4 HR3 0.10
!GROUP
!ATOM C C 0.51
!ATOM O O -0.51
BOND C5 H5 N1 C5 C2 N1
BOND N3 C4
BOND N1 HN1 C4 H4 C2 H2
DOUBLE C5 C4 C2 N3
IMPR N1 C5 C2 HN1 C4 C5 N3 H4 C2 N1 N3 H2
IMPR N1 C2 C5 HN1 C4 N3 C5 H4 C2 N3 N1 H2
!IMPR N -C CA HN C CA +N O
!CMAP -C N CA C N CA C +N
!DONOR HN N
DONOR HN1 N1
ACCEPTOR N3
!ACCEPTOR O C
!IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
!IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
!IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
!IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
!IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
!IC N C *CA H5 1.4521 107.7000 122.4600 109.9900 1.5519
!IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
!IC N CA H5 C5 1.4521 112.1200 180.0000 114.0500 1.5041
!IC C5 CA *H5 HB1 1.5041 114.0500 121.1700 109.0100 1.1118
!IC C5 CA *H5 HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
!IC CA H5 C5 N1 1.5519 114.0500 90.0000 124.1000 1.3783
!IC N1 H5 *C5 C4 1.3783 124.1000 -171.2900 129.6000 1.3597
!IC H5 C5 N1 C2 1.5041 124.1000 -173.2100 107.0300 1.3549
!IC H5 C5 C4 N3 1.5041 129.6000 171.9900 110.0300 1.3817
IC N3 N1 *C2 H2 1.3166 111.6300 -179.6300 123.8900 1.0932
IC C2 C5 *N1 HN1 1.3549 107.0300 -174.6500 126.2600 1.0005
IC N3 C5 *C4 H4 1.3817 110.0300 -177.8500 129.6300 1.0834