AMBER Archive (2007)

Subject: AMBER: Box problems in vacuum minimization with sander.serial 8

From: j j (fantvamp_at_gmail.com)
Date: Tue Feb 13 2007 - 13:05:16 CST

Dear Amber Users,
I'm trying to carry out a very simple minimization.
For this purpose I'm using the following flags:
Minimization
 &cntrl
   imin=1, ntr=0,
   cut=6, ntpr=100, scee=1.2, drms=0.0001,
   maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25,
   dielc = 4.0,
 &end
After getting the topology and coord file from xleap,
I try to launch sander8.serial and I got the following errors:
a) If I do not set a box sander start running but do not
print any result while one processor is at 100%.
I've obtained RU5.topology RU5.coord from leaprc.ff99,
just making saveamberparm RU5 or NSER.
b) If I set a box:
setbox NSER centers
,and get the coord and top files the results are:
==> NSER.outm1 <==
 Here is the input file:

Minimization
 &cntrl
   imin=1, ntr=0,
   cut=6, ntpr=100, scee=1.2, drms=0.0001,
   maxcyc= 3000, ntmin=1, ncyc=1000, nsnb=25,
   dielc = 4.0,
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 1.511

 PARAMETER RANGE CHECKING:
 parameter nfft1: (grid size) has value 4
 This is outside the legal range
 Lower limit: 6 Upper limit: 2048
 The limits may be adjustable; search in the .h files
c) So I edit the box dimensions to 16 16 16 and
I got:
[...]
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 Exceeding lastrst in get_stack
   lastrst = 11618
   top_stk= 0
   isize = 21281
   request= 21281
  Increase lastrst in the &cntrl namelist

I think I would set the box size at least twince the cut off.
If I run this same flags for a big system it runs fine.
How can I run this minimization just for a single residue?.

Thank you,
JJ


  • application/octet-stream attachment: RU5.min1

  • application/octet-stream attachment: RU5.outm1

  • application/octet-stream attachment: NSER.min1


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