I don't understand the reasons why, but I think belly does not
properly work within the GB method in sander, so the results will likely
be pretty strange. I don't have a manual handy but hopefully it
contains a warning to that effect. On the other hand I've had good success
using cartesian restraints with GB. As a side note, belly certainly will
not work properly with the constant pressure option, whereas again
cartesian restraints are ok with constant pressure. My sense is that
belly is an option that will go away sometime in a future release, but
that cartesian restraints are here for the longterm.
hope this helps
Tom D
On Wed, 7 Aug 2002, Giulio Rastelli wrote:
>
> Dear all,
> I am running an MD simulation of a protein using the GB-SA model (amber7 on
> a IBM-SP3 computer).
> Unexpectedly, the simulation works fine when I let everything free to move.
> Instead, when I define a subset
> of residues allowed to move (ibelly=1) the residues of the belly shift more
> the 60Angs apart from the rest
> of the protein, with consequent blow up of the energy! Is it correct to use
> belly with GB-SA?
> The problem occurs both using single of more processors, as well as using
> SGI instead of SP3.
> It occurs also by using igb=1 only, and *not* igb=1, gbsa=1, saltcon=1 as
> in the following input file.
> Help is very appreciated,
> Giulio Rastelli
>
> Here is my input file:
>
> DYNAMICS with GB-SA
> &cntrl
> nmropt=1,
> ibelly=1,
> imin=0, nstlim=100000, dt=0.002, temp0=300.0, ntt=1,
> ntx=1, ntpr=100,
> ntf=2, ntc=2, ntb=0, igb=1, gbsa=1, saltcon=0.1, cut=10.0, scee=1.2,
> nsnb=25, ntwx=100,
> &end
> &wt type='TEMP0', istep1=1,istep2=5000,value1=0.,
> value2=300., &end
> &wt type='END' &end
> &rst iat=0, &end
> Belly 8A
> RES 12
> RES 16
> RES 19
> RES 37 49
> RES 52
> RES 59
> RES 67 68
> RES 81 105
> RES 121 132
> RES 138 144
> RES 146
> RES 152
> RES 173 178
> RES 214
> RES 215 218
> END
> END
>
> And here is a sample of output. After less than 1ps the EGB and ESURF
>
> contributions go out of range, the same happens to BOND because the
>
> bonds between the belly and non-belly atoms are broken:
>
> NSTEP = 800 TIME(PS) = 1.600 TEMP(K) =********* PRESS = 0.0
> Etot = nan EKtot = 5020605.6000 EPtot = nan
> BOND = ************ ANGLE = 5113.4269 DIHED = 1090.6565
> 1-4 NB = 260.5515 1-4 EEL = 3135.9864 VDWAALS = -611.0062
> EELEC = -5191.9635 EGB = nan RESTRAINT = 0.0000
> ESURF = nan
>
Received on Wed Aug 07 2002 - 04:58:17 PDT
