Dear Zora,
I did some integrations from something in vacuum to nothing, but I didn't
use the option ifsc=2, because it was not clear to me how it works and what
it was doing. So I chose to use ifsc=1, and made everything in the system
disappear but one residue.
In your specific case, if you have a molecule with 7 residues, I would start
with the full molecule, and apply the charge mask to the 7 residues, but the
soft core mask to 6 of the 7 residues. In this way, you end up with only one
residue in vacuum, without charge.
I don't know exactly what you want to calculate, but this may be a good
option for you.
Regards,
Ignacio
On Wed, May 25, 2011 at 9:32 AM, Zora Strelcova <stre.chemi.muni.cz> wrote:
> Dear Amber users,
>
> I would like to pertube system (7 residues) in vacuum to nothing, but I am
> forcing several problems:
>
> My first calculations were performed in Amber 10 with the option ifsc=2 and
> following input:
>
> &cntrl
> imin=0,
>
> nstlim=200000,
> dt=0.001,
> irest=1,
> ntx=5,
>
> ntpr=1000,
> ntwx=1000,
> ntwr=1000,
> ioutfm=1,
>
> ig=RANDOM,
> ntf=1,
> ntb=0,
> cut=20,
>
> ntr=1,
>
> icfe=0,
> clambda=LAMBDA,
> ntc=2,
> ifsc=2,
> crgmask='CRGMASK',
> scmask='SCMASK',
> &end
> Hold the system fixed by restraints
> 50
> RES 1 7
> END
> END
>
> In my run script I am changing the masks according to the system (here
> SCMASK=:1-7), and LAMBDA according to the current window.
>
> All the simulations end with the error report:
>
>
> Frac coord min, max: 0.167951042129902 1.00004556442007
> The system has extended beyond
> the extent of the virtual box.
> Restarting sander will recalculate
> a new virtual box with 30 Angstroms
> extra on each side, if there is a
> restart file for this configuration.
> SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> Atom out of bounds. If a restart has been written,
> restarting should resolve the error
>
>
> Can you help me please to fix this problem?
>
> On the other hand, I would like to run all TI simulations in amber 11.
> Since
> ifsc=2 option is no more implemented in this version, I would like to ask,
> how to set up such simulation. I have tried to prepare empty restart file
> and empty topology file representing process V1, but I did not work.
>
> Thank you for you suggestions, Zora
> --
> ==========================================
> Zora Strelcova
> ==========================================
> National Centre for Biomolecular Research (NCBR)
> Faculty of Science, Masaryk University
> Kotlarska 2, 611 37 Brno, Czech Republic
> =========================================
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>
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Received on Wed May 25 2011 - 07:30:02 PDT
