AMBER Archive (2008)

Subject: Re: AMBER: "radius = 0.000"

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Tue Jul 01 2008 - 12:17:54 CDT

Hi,
So, here is the answers:

2 Bob Duke:
    A. I have done input in "true" float for cut-off - the same problem.

    Q. One simple thing to check - is your compiler indeed converting
the integer input value for "cut" to float correctly (should be apparent
from the listing of used values in the mdout file). I actually don't
know what the spec says should happen a namelist on this, but the intel
compiler will do the correct conversion for you; most folks I believe
would bother to specify 12.0 in the mdin for cut. This may not be it at
all; other worries would be if the input prmtop/inpcrd from leap are
actually what you think they are (for a solvated system).

2 Thomas Steinbrecher:
    A. My prmtop contains "1" - so systems setup done as periodic:
       0 0 0 0 0 0 0 1
26 0
   However: minimization restart (output) file contains no dimension
info. The DNA turorial examples does the same, but runs w/ no problem.

2 Carlos Simmerling
    A. I have run just DNA tutor case - it was OK. AMBER after
compilation passed all tests (parallel and serial, g95 compiler, AMBER
9, Xeon, Redhat, gcc 3.x).
    Q. have you run all of the test cases?
    Q. did they work without error?

    A. My system is simple protein with standard amino acids, no
modifications, no extra topologies. System contains that protein, water
(TIP3P) and one Sodium ion. No restrains, no fixed particles = just
"plain" MD.
    Q. is there anything unusual about your system- just standard
protein and water?

    A. Here is my essential build steps:
            parm99 = loadamberparams parm99.dat
            pdb = loadpdb "1T29.pdb"
            addions pdb Na+ 0
            solvatebox pdb TIP3PBOX 10.0
            saveamberparm pdb BRCT.prmtop BRCT.inpcrd
            During the build there was no errors, just warnings
including a long 3.2A distance between atoms on backbone, reconstructed
missing atom in residues.
    Q. you might give us some info from leap on how you built it, and

    A. The restart file taken from minimization, where the input of job
setup was taken from DNA tutorial. That restart file contains no box
dimensions and velocities ( as DNA tutorial does - the same).
    Q. also what kind of simulation gave you the restart file.

Thank you for your input and patience. It seems that my migration to
AMBER needs some time ...

Arturas

Some update:
After minimization it seems there are no velocities and box size (the
last line) in a restart file. However, say DNA test in AMBER tutor
worked fine and those lines are present.

Carlos Simmerling wrote:
> a few things to check first:
> have you run all of the test cases?
> did they work without error?
> is there anything unusual about your system- just standard protein and water?
> you might give us some info from leap on how you built it, and
> also what kind of simulation gave you the restart file.
>
> On Tue, Jul 1, 2008 at 12:08 PM, Arturas Ziemys
> <arturas.ziemys_at_uth.tmc.edu> wrote:
>
>> Hi,
>>
>> I have minimized my pretty simple protein+water system. Supplied minimized
>> structure (from restart output) to equilibration. My job was hanging
>> forever. Using '-o stdout' I saw that my job stalled at after that line is
>> printed: "sphere to fit in unit cell has radius = 0.000".
>>
>> I have tried to find some answer on internet but without success - just one
>> similar question. My feeling says that job does not know my systems
>> dimensions ? What is the remedy ?
>>
>> job setup:
>> &cntrl
>> imin = 0,
>> ntx = 1,
>> irest = 0,
>> ntt = 3,
>> gamma_ln = 1.0,
>> temp0 = 300.0,
>> tempi = 300.0,
>> ntp = 1,
>> ntb = 2,
>> ntf = 2,
>> ntc = 2,
>> cut = 12,
>> dt = 0.001,
>> nstlim = 100
>> /
>>
>>
>> --
>>
>> Arturas Ziemys, PhD
>> School of Health Information Sciences
>> University of Texas Health Science Center at Houston
>> 7000 Fannin, Suit 880
>> Houston, TX 77030
>> Phone: (713) 500-3975
>> Fax: (713) 500-3929
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>>
>>
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-- 

Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  

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