AMBER: Volume of ucell too big

From: Atsutoshi Okabe <okabe.cherry.bio.titech.ac.jp>
Date: Sat, 16 Dec 2006 17:41:43 +0900

Dear all,

 

I executed sander program to equilibrate the system in methane solvent box.

But I got the following error message in output file.

 

NSTEP = 32400 TIME(PS) = 78.800 TEMP(K) = 296.90 PRESS =
116.7

 Etot = 3409.4640 EKtot = 2349.6920 EPtot =
1059.7720

 BOND = 10.2431 ANGLE = 1222.7808 DIHED =
51.9193

 1-4 NB = 10.1691 1-4 EEL = 140.2031 VDWAALS =
-256.9207

 EELEC = -137.2042 EHBOND = 0.0000 RESTRAINT =
18.5814

 EAMBER (non-restraint) = 1041.1905

 EKCMT = 628.4852 VIRIAL = 149.0902 VOLUME =
190305.2399

                                                   Density =
0.1032

 Ewald error estimate: 0.1011E-01

 
---------------------------------------------------------------------------- 
--
 
 SANDER BOMB in subroutine nonbond_list
  volume of ucell too big, too many subcells
  list grid memory needs to be reallocated, restart sander
 
 
 
I can't understand why I got the error message.
But actually, I got the following warning message in tleap.
(Solvent has no box, so preparing by making box including vdw)
 
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> source tleap
----- Source: ./tleap
----- Source of ./tleap done
Loading parameters: ./HEP.ff
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Prep file: ./HEP.prep
Loading parameters: ./TRE.ff
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Prep file: ./TRE.prep
Loading PDB file: ./CIS_HEP_TRE.pdb
 (starting new molecule for chain B)
  total atoms in file: 64
Loading parameters: ./MET.ff
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Prep file: ./MET.prep
Loading PDB file: ./MET_HF_6-31g_opt.pdb
  total atoms in file: 5
Solvent has no box, so preparing by making box including vdw
(Use 'setBox centers' first if box was pre-equilibrated)
  Solute vdw bounding box:              12.168 12.838 11.434
  Total bounding box for atom centers:  40.168 40.838 39.434
  Solvent unit box:                     4.510 4.748 4.481
  Total vdw box size:                   40.590 42.732 40.329 angstroms.
  Volume: 69950.323 A^3 
  Total mass 11828.282 amu,  Density 0.281 g/cc
  Added 710 residues.
 
Is its message caused the sander error message like above?
 
Could you please give me any suggestions to solve this problem?
 
Thank you
 
Atsutoshi
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Received on Sun Dec 17 2006 - 06:07:26 PST
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