AMBER Archive (2004)

Subject: AMBER: How to use these parameters?

From: scopio (scopio_at_163.com)
Date: Tue Mar 16 2004 - 19:15:15 CST

Dear AmberUsers:

I have a pdb contains some residue that could not be recognized by xleap
due to lacking of amber parameters. Fortunately, I get these parameters
from a very kind person. But I don't know how to use them. Could anybody
check them attached and give me some suggestions? Thanks in advance!

By the way, is the mail reflector would filter email larger than 1MB?

Regards!

scopio


#
#
# quinone7.prm
# cromofo_last.prm
#
#
BOND
#fe+mg ( k from CHARMM; dist from X-ray)
nb fe 65.00 2.10
o2 fe 65.00 2.25
nb mgc 65.00 2.25
........................( igored )
END
BENDINGS
#fe+mg
cr nb mgc 0.00 0.00
nb mgc nmh 0.00 0.00
nb mgc ns 0.00 0.00
....................... ( igored )
END
TORSION PROPER
#fe
x fe nb x 0.00 4
x fe o2 x 0.00 4
....................... ( igored )
END
TORSION IMPROPER
x ccs ns mgc 1.100 2.0 180.0 cosine
x x nmh mgc 1.100 2.0 180.0 cosine
...................... ( igored )
END
NONBONDED MIXRULE
#fe
fe 0.740 0.250 0.740 0.250 55.847
#my
mgc 0.650 0.250 0.000 0.000 24.305
nh 1.824 0.170 0.000 0.000 14.010
ns 1.824 0.170 0.000 0.000 14.010
...................... ( igored )
END

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
............. ( igored )
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
................ ( igored )
imphd
#
c1b c4b nb mg
c2b nb c1b chb
c1b c3b c2b cmb
c4b c2b c3b cab
c3b nb c4b chc
................ ( igored )
end

termatom * *
RESIDUE_END

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