AMBER Archive (2006)

Subject: AMBER: building a box

From: kepa koldo burusco (kepaquestions_at_yahoo.es)
Date: Tue Nov 07 2006 - 10:52:28 CST

[7-XI-2006]
   
  Hi amber users!!!
   
  I am trying to do something apparently "wierd" and amber gives me problems all the time.
   
  I have built up a molecule made of 5 units. One is the central unit, and the other 4 are linked to that one. We are trying to study the bulk behaviour of a liquid enterely made from molecules of the same type. I mean, we are trying to create a solvent box surrounding our molecule with lots of molecules of the same type. We have been doing this with xLEaP typing:
   
       solvatebox new_petLin new_bPl 10.0
   
  and also
   
       solvateDontClip new_petLin new_bPl 10.0
   
  (new_petLin and new_bPl are "the same molecule", the different unit names are to allow easier ptraj analysis after running Molecular Dynamics)
   
  We have tried to enlarge/reduce the box size, to change the molecular conformation (unfolded/folded), to use different versions of xLEaP (amber 7 version and amber 8 version)... and each time we get an error message similar to the one attachd to this mail:
   
  The "solvent" molecules directly surrounding the "solute" molecule appear laking some residues due to avoid molecular overlaping, so on new "wierd" links are created among distant molecules.
   
  It seems that se algorithm that solvates molecules expect the solvent to be a single-unit molecule...
   
  We have also tried to delete the problematic molecules directly from the box aided by xLEaP windows tools once created, but "unfortunately" the software complains, xLEaP exists and the shell shows a "segmentation fault" message...
   
  So... any idea? any help? anybody knows how I could build my box avoiding problems such as these???
   
  Thank you very much in advance for your help.
   
   
  Kepa K. Burusco
  PhD Student
  Universidad Autonoma de Barcelona
  BARCELONA (Spain)

                 
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Welcome to LEaP!
Sourcing leaprc: ./leaprc
----- Source: /usr/local/amber7/dat/leap/cmd/leaprc.ff99
----- Source of /usr/local/amber7/dat/leap/cmd/leaprc.ff99 done
Log file: ./leap.log
Loading parameters: ./parm99.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib
Loading parameters: ./extraParamIQLasem.par
Reading force field mod type file (frcmod)
Loading library: ./kepa.lib
Loading library: ./IQLasem_fold.lib
Loading library: ./glum.lib
Loading library: ./itz.lib
> solvateDontClip new_petLin new_bPl 10.0
Solvent has no box, so preparing by making box including vdw
(Use 'setBox centers' first if box was pre-equilibrated)
  Solute vdw bounding box: 20.017 19.249 19.388
  Total bounding box for atom centers: 40.017 39.249 39.388
  Solvent unit box: 20.130 17.947 16.051
  Total vdw box size: 40.260 53.841 48.153 angstroms.
  Volume: 104378.304 A^3
  Total mass 20823.218 amu, Density 0.331 g/cc
  Added 83 residues.
> saveamberparm new_petLin box_petLin.top box_petLin.crd
Checking Unit.
WARNING: There is a bond of 16.971215 angstroms between:
------- .R<li2 26>.A<C3 1> and .R<li2 28>.A<C3 1>
WARNING: There is a bond of 23.170284 angstroms between:
------- .R<li2 67>.A<C3 1> and .R<li2 71>.A<H24 35>
WARNING: There is a bond of 14.589751 angstroms between:
------- .R<li2 68>.A<C3 1> and .R<li2 71>.A<H13 17>
ERROR: The unperturbed charge of the unit: 1.335000 is not integral.
WARNING: The unperturbed charge of the unit: 1.335000 is not zero.

 -- ignoring the error and warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: CT - HC - CT
Could not find angle parameter: CT - HC - CT
Building proper torsion parameters.
 ** No torsion terms for CT-CT-HC-CT
 ** No torsion terms for HC-CT-HC-CT
 ** No torsion terms for HC-CT-HC-CT
 ** No torsion terms for CT-HC-CT-HC
 ** No torsion terms for CT-HC-CT-CT
 ** No torsion terms for CT-HC-CT-CT
 ** No torsion terms for CT-CT-HC-CT
 ** No torsion terms for HC-CT-HC-CT
 ** No torsion terms for HC-CT-HC-CT
 ** No torsion terms for CT-HC-CT-HC
 ** No torsion terms for CT-HC-CT-CM
 ** No torsion terms for CT-HC-CT-CT
Building improper torsion parameters.
 total 352 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.

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