AMBER Archive (2004)

Subject: Re: AMBER: exclusion list

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Mon Oct 11 2004 - 10:26:20 CDT

Some more information on my test ...

I checked the excluded atom list section of another system with no bonds
(Lennard-Jones particles). The NUMBER_EXCLUDED_ATOMS section is all 1s
for every particle, not zero. The EXCLUDED_ATOMS_LIST section is all
zeros. So I made corresponding changes to my test system (which I think
is not the key), and again the VDW energy term is zero. I checked the
modified prmtop with rdparm: printexcluded and it confirmed there is no
excluded atoms. What am I missing here? I attached the modified prmtop.
Your help is appreciated.

Guanglei

Guanglei Cui wrote:
> Dear all,
>
> Is there a way to turn off the exclusion and include the nonbond energy
> among bonded atoms? I tried to mark NUMBER_EXCLUDED_ATOMS section in
> prmtop with all zeros? But there was no VDW energy in the output.
>
> Thanks.
>
> Regards,
>
> Guanglei
>
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%VERSION VERSION_STAMP = V0001.000 DATE = 10/07/04 11:32:44
%FLAG TITLE
%FORMAT(20a4)
                                                                                
%FLAG POINTERS
%FORMAT(10I8)
       3 1 0 2 0 1 0 0 0 0
       4 1 2 1 0 1 1 0 1 0
       0 0 0 0 0 0 0 0 3 0
       0
%FLAG ATOM_NAME
%FORMAT(20a4)
ME1 ME2 ME3
%FLAG CHARGE
%FORMAT(5E16.8)
  0.00000000E+00 0.00000000E+00 0.00000000E+00
%FLAG MASS
%FORMAT(5E16.8)
  4.50600000E+01 4.50600000E+01 4.50600000E+01
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
       1 1 1
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
       1 1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
       1
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
UNK
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
       1
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
  8.95000000E+00
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
  3.20000000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
  3.00000000E-03
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
  2.28289164E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)

%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)

%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)

%FLAG SOLTY
%FORMAT(5E16.8)
  0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
  6.26331456E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
  6.08289587E+02
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)

%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
       0 3 1 3 6 1
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)

%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
       0 3 6 1
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)

%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)

%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
       0 0 0 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)

%FLAG HBOND_BCOEF
%FORMAT(5E16.8)

%FLAG HBCUT
%FORMAT(5E16.8)

%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
ME ME ME
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
BLA BLA BLA
%FLAG JOIN_ARRAY
%FORMAT(10I8)
       0 0 0
%FLAG IROTAT
%FORMAT(10I8)
       0 0 0
%FLAG RADII
%FORMAT(5E16.8)
  1.50000000E+00 1.50000000E+00 1.50000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
  8.00000000E-01 8.00000000E-01 8.00000000E-01

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