AMBER Archive (2008)

Subject: AMBER: shake the molecule

From: amit jain (
Date: Fri Oct 03 2008 - 00:26:33 CDT

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

I tried to make input file as follows

   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,
   ntr=0, dt=0.001, ig=323657,
   noshakemask=':6-120_at_C=,O=,N=,S= & !@H=',
   ew_type=0, dsum_tol=0.000001
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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