Dear list,
I am confused on the following commands in 24.11.5 of amber 16 manual (P481)"
# 1) Define two centers of mass. COM1 is defined by
# {C1 in residue 1; C1 in residue 2; N2 in residue 3; C1 in residue 4}.
# COM2 is defined by {C4 in residue 1; O4 in residue 1; N* in residue 1}.
# (These definitions are effected by the igr1/igr2 and grnam1/grnam2
# variables; You can use up to 200 atoms to define a center-of-mass
# group)
# 2) Set up a distance restraint between COM1 and COM2 which goes from a
# target value of 5.0A to 2.5A, with a force constant of 1.0, over steps 1-5000.
#
&rst iat=-1,-1, nstep1=1,nstep2=5000,
iresid=1,irstyp=0,ifvari=1,ninc=0,imult=0,ir6=0,ifntyp=0,
r1=0.00000E+00,r2=5.0000,r3=5.0000, r4=99.000,rk2=1.0000,rk3=1.0000,
r1a=0.00000E+00,r2a=2.5000,r3a=2.5000, r4a=99.000,rk2a=1.0000,rk3a=1.0000,
igr1 = 2,3,4,5,0, grnam1(1)='C1',grnam1(2)='C1',grnam1(3)='N2',
grnam1(4)='C1', igr2 = 1,1,1,0, grnam2(1)='C4',grnam2(2)='O4',grnam2(3)='N*',
/
what is 2,3,4,5,0 and what is i in grnam1(i)?
Thank you,
Ming
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Received on Wed Jul 20 2016 - 06:30:03 PDT
