Hello,
I have a system of 10,000 water, 115 Amino acid (5 chain of 23 Amino acid
sequence) and 5 solute molecule.
It is desired to SHAKE all the bonded H atom of WATER and all Amino acids.
In addition to that it is require to SHAKE all internal bonds in solute
molecule.
I tried to make input file as follows
&cntrl
imin=0,
ntx=1, irest=0, ntpr=100, ntwr=500, ntwx=500,
ntwe=500, ntf=2, ntb=1, nstlim=250000, iwrap=1,
temp0 = 300.0, tempi=300.0, ntt=2, tautp=1.0,
ntp=0, pres0=1.0, comp=44.6,
taup=2.0, ntc=3,
ntrx=1,
ntr=0, dt=0.001, ig=323657,
noshakemask=':6-120.C=,O=,N=,S= & !.H=',
&end
&ewald
ew_type=0, dsum_tol=0.000001
&end
END
With ntc=3, first all the bonds in the system are employed SHAKE.
then Amino acid chains (residue 6 to 120) was put under noshakemask, except
Hydrogen atoms.
But it doesnt help, because C,N,O, S also makes bond with H.
So it removes SHAKE constraint such as
Removing shake constraints from CD2 TYR 6 -- HD2 TYR 6
Removing shake constraints from CE2 TYR 6 -- HE2 TYR 6
Removing shake constraints from OH TYR 6 -- HH TYR 6
Removing shake constraints from CE1 TYR 6 -- HE1 TYR 6
-
blah blah
-
Removing shake constraints from C TYR 6 -- O TYR 6
Removing shake constraints from C TYR 6 -- N TYR 7
Removing shake constraints from CE2 TYR 6 -- CD2 TYR 6
Removing shake constraints from CZ TYR 6 -- OH TYR 6
-
blah blah
-
The second part is what needed (but not first one involving H*),
Can you please suggest me on noshakemask flags in input file, or some other
way to get the specifics of the system incorporated in MD?
thanks a lot
Amit Jain
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Received on Fri Oct 03 2008 - 05:12:25 PDT
