On Tue, May 26, 2015, Evgenia Dueva wrote:
>
> I try to run sander (Amber12) on several processors with following
> parameters:
>
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 8.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 310.0, temp0 = 310.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 500000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 1000
> /
>
> but I have an error message, if I choose more than 8 processors:
>
> partition error in shake on processor 0
> this processor has atoms 1 through 12072
> atom 12072 is within this range
> atom 12073 is not within this range !
>
>
> My system consist of glycosylated protein and two ligand molecules in
> explicit water, atom 12072 is a carbon and 12073 is a hydrogen of first
> ligand.
Sander is somehow confused about which residue is which. Use ambpdb to create
a pdb file from your input coordinates and prmtop file. Look at atoms 12072
and 12073: are they in the same residue? Does anything else look odd in about
the ligands? Is there a TER card between the protein and the ligands?
The simple workaround (if possible) is to use pmemd: running sander on more
than 8 threads may not help much, and pmemd should be considerably faster
(assuming you have a good interconnect among threads.)
If pmemd is not an option, and looking at the pdb file doesn't help, you will
probably have to post your prmtop and coordinate files so that we can try to
reproduce the problem.
...dac
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Received on Tue May 26 2015 - 08:30:02 PDT
