Dear AMBER users:
I was tring to get amber parameters for Bacterial Photosynthesis and
fortunately got amber-like paramters which is used in ORAC developed by
Dr. Massimo Marchi and Dr. P. Procacci.(
http://srv.chim.unifi.it/orac/)
Their force field file(frcmod) is the same as those in AMBER and can be
recognized by xleap. But the topology file in ORAC is much different
with AMBER's prepi file. ORAC's topology file only contains charges,
bond informations, improper torisions as well as atom name and type
consist with the name in PDB and its force field file respectively.
Now, my problem is how to convert this topology file to amber prepi
format. Attached are part(one residue) of ORAC's topology file and
corresponding part of PDB file. Hope anyone who have an idea could give
me light! Thanks in advance!
Best Regards and have a nice weekend!
Liu
RESIDUE bcl ( Total Charge = 0.0 )
atoms
group
mg mgc 0.1340
group
cha csb 0.0650
group
chb cab -0.2240
hb ha0 0.1150
group
chc cab -0.2730
hc ha0 0.1680
group
chd cab -0.2620
hd ha0 0.1470
group
na ns 0.0360
c1a ccs -0.1190
c4a ccs -0.0370
group
c2a ct1 0.0910
h2a hc 0.0080
group
c3a ct1 0.2620
h3a hc -0.0160
group
cma ct3 -0.2750
hma1 hc 0.0700
hma2 hc 0.0700
hma3 hc 0.0700
group
caa ct2 -0.0630
haa1 hc 0.03802
haa2 hc 0.03802
group
cba ct2 -0.2310
hba1 hc 0.08302
hba2 hc 0.08302
group
cga c2a 0.6610
o1a o2c -0.5210
group
o2a o1c -0.3250
group
nb nmh -0.0550
c1b crb -0.0270
c4b cnb 0.1980
group
c2b cbb 0.1990
c3b cbb -0.4180
group
cmb ct3 -0.2380
hmb1 hc 0.08133
hmb2 hc 0.08133
hmb3 hc 0.08133
group
cab c2e 0.6950
obb o2c -0.5370
group
cbb ct3 -0.3920
hbb1 hc 0.10333
hbb2 hc 0.10333
hbb3 hc 0.10333
group
nc ns 0.0720
c1c ccs -0.0880
c4c ccs -0.0630
group
c2c ct1 0.3080
h2c hc -0.0140
group
c3c ct1 0.0680
h3c hc 0.0150
group
cmc ct3 -0.3010
hmc1 hc 0.07233
hmc2 hc 0.07233
hmc3 hc 0.07233
group
cac ct2 0.0640
hac1 hc 0.0050
hac2 hc 0.0050
group
cbc ct3 -0.2510
hbc1 hc 0.05766
hbc2 hc 0.05766
hbc3 hc 0.05766
group
nd nmh 0.0650
c1d cpb -0.0500
c4d cqb -0.1310
group
c2d cbb 0.2270
c3d cbb -0.2390
group
cmd ct3 -0.3070
hmd1 hc 0.09633
hmd2 hc 0.09633
hmd3 hc 0.09633
group
cad c2k 0.5420
obd o2c -0.5100
group
cbd ct1 -0.2020
hbd hc 0.0710
group
cgd c2a 0.7350
o1d o2c -0.5390
group
o2d o1c -0.4890
group
ced ct3 0.0150
hed1 hc 0.06633
hed2 hc 0.06633
hed3 hc 0.06633
#
group
c1 ct2 0.39299
h11 hc 0.0065
h12 hc 0.0065
group
c2 cqq -0.342
h21 ha0 0.133
group
c3 cq2 0.055
group
c4 ct3 -0.301
h41 hc 0.092666
h42 hc 0.092667
h43 hc 0.092667
group
c5 ct2 0.098
h51 hc 0.0075
h52 hc 0.0075
group
c6 ct2 -0.18
h61 hc 0.09
h62 hc 0.09
group
c7 ct2 -0.18
h71 hc 0.09
h72 hc 0.09
group
c8 ct1 -0.09
h81 hc 0.09
group
c9 ct3 -0.27
h91 hc 0.09
h92 hc 0.09
h93 hc 0.09
group
c10 ct2 -0.18
h101 hc 0.09
h102 hc 0.09
group
c11 ct2 -0.18
h111 hc 0.09
h112 hc 0.09
group
c12 ct2 -0.18
h121 hc 0.09
h122 hc 0.09
group
c13 ct1 -0.09
h131 hc 0.09
group
c14 ct3 -0.27
h141 hc 0.09
h142 hc 0.09
h143 hc 0.09
group
c15 ct2 -0.18
h151 hc 0.09
h152 hc 0.09
group
c16 ct2 -0.18
h161 hc 0.09
h162 hc 0.09
group
c17 ct2 -0.18
h171 hc 0.09
h172 hc 0.09
group
c18 ct1 -0.09
h181 hc 0.09
group
c19 ct3 -0.27
h191 hc 0.09
h192 hc 0.09
h193 hc 0.09
group
c20 ct3 -0.27
h201 hc 0.09
h202 hc 0.09
h203 hc 0.09
end
bonds
nb mg nc mg nd mg na mg
nb c1b c1b c2b c2b c3b c3b c4b
c4b nb
nc c1c c1c c2c c2c c3c c3c c4c
c4c nc
nd c1d c1d c2d c2d c3d c3d c4d
c4d nd
na c1a c1a c2a c2a c3a c3a c4a
c4a na
c4b chc chc c1c c4c chd chd c1d
c4d cha cha c1a c4a chb chb c1b
chb hb chc hc chd hd
c2b cmb cmb hmb1 cmb hmb2 cmb hmb3
c3b cab cab obb
cab cbb cbb hbb1 cbb hbb2 cbb hbb3
c2c h2c c2c cmc
cmc hmc1 cmc hmc2 cmc hmc3
c3c h3c c3c cac cac hac1 cac hac2
cac cbc cbc hbc1 cbc hbc2 cbc hbc3
c2d cmd cmd hmd1 cmd hmd2 cmd hmd3
c3d cad cad obd cad cbd cbd cha
cbd hbd cbd cgd cgd o1d cgd o2d
o2d ced ced hed1 ced hed2 ced hed3
c3a h3a c3a cma
cma hma1 cma hma2 cma hma3
c2a h2a c2a caa caa haa1 caa haa2
caa cba cba hba1 cba hba2
cba cga cga o1a cga o2a
o2a c1 c1 h11 c1 h12
#
c1 c2 c2 h21 c2 c3
c3 c4 c4 h41 c4 h42 c4 h43
c3 c5 c5 h51 c5 h52
c5 c6 c6 h61 c6 h62
c6 c7 c7 h71 c7 h72
c7 c8 c8 h81
c8 c9 c9 h91 c9 h92 c9 h93
c8 c10 c10 h101 c10 h102
c10 c11 c11 h111 c11 h112
c11 c12 c12 h121 c12 h122
c12 c13 c13 h131
c13 c14 c14 h141 c14 h142 c14 h143
c13 c15 c15 h151 c15 h152
c15 c16 c16 h161 c16 h162
c16 c17 c17 h171 c17 h172
c17 c18 c18 h181
c18 c19 c19 h191 c19 h192 c19 h193
c18 c20 c20 h201 c20 h202 c20 h203
end
imphd
#
c1b c4b nb mg
c2b nb c1b chb
c1b c3b c2b cmb
c4b c2b c3b cab
c3b nb c4b chc
#
c1c nc c4c mg
nc c2c c1c chc
nc c3c c4c chd
#
c1d c4d nd mg
c2d nd c1d chd
c1d c3d c2d cmd
c4d c2d c3d cad
c3d nd c4d cha
#
c1a na c4a mg
na c2a c1a cha
na c3a c4a chb
#
c4d cbd cha c1a
c1b c4a chb hb
c1c c4b chc hc
c1d c4c chd hd
#
c3b cbb cab obb
c3d cbd cad obd
cbd cgd o1d o2d
cba cga o1a o2a
#
c3 c1 h21 c2
c5 c2 c4 c3
end
termatom * *
RESIDUE_END
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Received on Fri May 14 2004 - 13:53:00 PDT
