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mittko Offline OP
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I looked into all par and top CHARMM files and did not find any parameters for a nitro-group. It seems that this group has not been parametrized yet. Other people asked in the forum for parameters for molecules containing this group some time ago, so I was wondering about if since then people have parametrized and/or found a way to parametrize this group.

Also, a somehow related question is: do atom types like NPP and NO2 exist in the current CHARMM force field? I cannot find such, but I may be missing some top/par files.
Thanks.

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we've recently optimized parameters for nitrobenzene, they follow. the charmm force fields are limited to biological related molecules, but we are working to extend it to a wider range of compounds. see me web page for details about optimizing parameters that are not available.

MASS 107 NG2O1 14.00700 ! NITB, nitrobenzene
MASS 155 OG2N1 15.99900 ! NITB, nitrobenzene

RESI NITB 0.000 ! nitrobenzene
GROUP !
ATOM C1 CG2R61 -0.18 !
ATOM H1 HGR61 0.16 ! H5 H4
ATOM C2 CG2R61 -0.115 ! \ ___ /
ATOM H2 HGR61 0.115 ! O6A C5---C4
ATOM C3 CG2R61 -0.115 ! \ + / \
ATOM H3 HGR61 0.115 ! - N6--C6 C3--H3
ATOM C4 CG2R61 -0.115 ! / \\ //
ATOM H4 HGR61 0.115 ! O6B C1---C2
ATOM C5 CG2R61 -0.18 ! / \
ATOM H5 HGR61 0.16 ! H1 H2
ATOM C6 CG2R61 0.32 !
ATOM N6 NG2O1 0.40 !
ATOM O6A OG2N1 -0.34 !
ATOM O6B OG2N1 -0.34 !
BOND C1 H1 C1 C2 C2 H2 C2 C3
BOND C3 H3 C3 C4 C4 H4 C4 C5 C5 H5 C5 C6
BOND C6 C1 C6 N6 N6 O6A N6 O6B
IC C2 C6 *C1 H1 0.0000 0.00 180.00 0.00 0.0000
IC C6 C1 C2 C3 0.0000 0.00 0.00 0.00 0.0000
IC C3 C1 *C2 H2 0.0000 0.00 180.00 0.00 0.0000
IC C1 C2 C3 C4 0.0000 0.00 0.00 0.00 0.0000
IC C4 C2 *C3 H3 0.0000 0.00 180.00 0.00 0.0000
IC C2 C3 C4 C5 0.0000 0.00 0.00 0.00 0.0000
IC C5 C3 *C4 H4 0.0000 0.00 180.00 0.00 0.0000
IC C6 C4 *C5 H5 0.0000 0.00 180.00 0.00 0.0000
IC C5 C1 *C6 N6 0.0000 0.00 180.00 0.00 0.0000
IC C1 C6 N6 O6A 0.0000 0.00 180.00 0.00 0.0000
IC O6A C6 *N6 O6B 0.0000 0.00 180.00 0.00 0.0000

MASS 107 NG2O1 14.00700 ! NITB, nitrobenzene
MASS 155 OG2N1 15.99900 ! NITB, nitrobenzene
CG2R61 NG2O1 230.00 1.4020 ! NITB, nitrobenzene
NG2O1 OG2N1 580.00 1.2250 ! NITB, nitrobenzene
CG2R61 CG2R61 NG2O1 20.00 120.00 ! NITB, nitrobenzene
CG2R61 NG2O1 OG2N1 65.00 116.00 ! NITB, nitrobenzene
OG2N1 NG2O1 OG2N1 105.00 128.00 ! NITB, nitrobenzene
CG2R61 CG2R61 CG2R61 NG2O1 2.0000 2 180.00 ! NITB, nitrobenzene
NG2O1 CG2R61 CG2R61 HGR61 1.0000 2 180.00 ! NITB, nitrobenzene
CG2R61 CG2R61 NG2O1 OG2N1 0.9000 2 180.00 ! NITB, nitrobenzene
NG2O1 0.0 -0.2000 1.8500 ! NITR, nitrobenzene
OG2N1 0.0 -0.1200 1.7000 ! NITR, nitrobenzene

alex


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mittko Offline OP
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Thanks.
I have a question though - are there improper angles in this residue that needs to be defined? Also, the atom types HGR61 and CG2R61 seem to be new ones, but are those corresponding to the types HP and CA, respectively?

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no improper. yes, the use of HP and CA is fine. alex


School of Pharmacy
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