On Thu, Jan 24, 2013 at 11:25 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear AMBER users,
>
> I am trying to run sander.MPI however I am getting strange error which is:
>
> rfree: End of file on unit 5
>
> Below I pasted my input file:
>
> pressure equilibration
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 9, ntr = 1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 25000, dt = 0.002,
> ntpr = 200, ntwx = 200, ntwr = 200
> /
> keep atoms restrained
> 5.0
> FIND
> C
> CA
> N
> O
> H
> SEARCH
> RES 1-445
> END
> EDN
>
In addition to Dan's comment about EDN, there are a number of issues with
this group-style input. First, each card in the "FIND" section should have
4 fields--they are described in the Amber manual. These fields MUST be
present -- with a * if you have no specific criteria. Second, the RES card
should not have a dash. Numbers are added in pairs representing a range.
So for you it should be:
RES 1 445
If you want only a single residue, it still needs to be a range. e.g.,
RES 1 1 445 445
will select only those 2 residues.
I was also thinking to use restraintmask= with restraint:wt=5 will be that
> different from that I pasted above?
>
I highly suggest that you use restraintmask and restraint_wt instead. The
only thing that the GROUP input can do that the restraintmask cannot is
assign different restraint weights to different parts of the system.
Unless that's what you want to do, the mask input is significantly simpler.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 24 2013 - 09:30:03 PST
