AMBER Archive (2006)

Subject: AMBER: Volume of ucell too big

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Sat Dec 16 2006 - 02:41:43 CST

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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