CHARMM Development Project
Posted By: Rohit hbond selection and interaction energy - 03/14/19 10:04 AM
Hi,

I am trying to get interaction energy of hydrogen bond. I am not sure why I am getting Positive energy values, these should have been negative.

below is the code as well as log file.
Code:
!==================================================
! Selection 
!==================================================
DEFINE donor sele bynum @IN1 SHOW END
set 1 ?SELRESI
set 2 ?SELTYPE
set 3 ?SELRESN
set 4 ?SELCHEM
set filename1 @1_@3_@2_@4

DEFINE acceptor sele bynum @IN2 SHOW END
set 1 ?SELRESI
set 2 ?SELTYPE
set 3 ?SELRESN
set 4 ?SELCHEM
set filename2 @1_@3_@2_@4

inte SELECT donor END SELECT acceptor SHOW END



log file
Code:
 CHARMM>    !==================================================
 CHARMM>    ! Selection
 CHARMM>    !==================================================
 CHARMM>    DEFINE donor sele bynum @IN1 SHOW END
 Parameter: IN1 -> "14"
 The following atoms are currently set:
SEGId RESId RESName  .. TYPEs ..
 PRT      2        TRP N       
 SELRPN>      1 atoms have been selected out of    218
  
 CHARMM>    set 1 ?SELRESI
 RDCMND substituted energy or value "?SELRESI" to "2"
 Parameter: 1 <- "2"
  
 CHARMM>    set 2 ?SELTYPE
 RDCMND substituted energy or value "?SELTYPE" to "N"
 Parameter: 2 <- "N"
  
 CHARMM>    set 3 ?SELRESN
 RDCMND substituted energy or value "?SELRESN" to "TRP"
 Parameter: 3 <- "TRP"
  
 CHARMM>    set 4 ?SELCHEM
 RDCMND substituted energy or value "?SELCHEM" to "NH1"
 Parameter: 4 <- "NH1"

CHARMM>    DEFINE acceptor sele bynum @IN2 SHOW END
 Parameter: IN2 -> "10"
 The following atoms are currently set:
SEGId RESId RESName  .. TYPEs ..
 PRT      1        SER OG      
 SELRPN>      1 atoms have been selected out of    218
  
 CHARMM>    set 1 ?SELRESI
 RDCMND substituted energy or value "?SELRESI" to "1"
 Parameter: 1 <- "1"
  
 CHARMM>    set 2 ?SELTYPE
 RDCMND substituted energy or value "?SELTYPE" to "OG"
 Parameter: 2 <- "OG"
  
 CHARMM>    set 3 ?SELRESN
 RDCMND substituted energy or value "?SELRESN" to "SER"
 Parameter: 3 <- "SER"
  
 CHARMM>    set 4 ?SELCHEM
 RDCMND substituted energy or value "?SELCHEM" to "OH1"
 Parameter: 4 <- "OH1"

CHARMM>    !==================================================
 CHARMM>    ! calculate energy of selection
 CHARMM>    !==================================================
 CHARMM>    inte SELECT donor END SELECT acceptor SHOW END
 SELRPN>      1 atoms have been selected out of    218
 The following atoms are currently set:
SEGId RESId RESName  .. TYPEs ..
 PRT      1        SER OG      
 SELRPN>      1 atoms have been selected out of    218
 INTER:  Normal Atom Nonbondselected           1 from a total of        8294
INTE ENR:  Eval#     ENERgy      Delta-E         GRMS
INTE EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
INTE>        1     27.29045      0.00000      0.67776
INTE EXTERN>       -0.02024     27.31069      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
Posted By: lennart Re: hbond selection and interaction energy - 03/14/19 10:18 AM
You are calculating the interaction energy between the two heavy atoms without including the all-important hydrogen.
Posted By: Rohit Re: hbond selection and interaction energy - 03/14/19 11:08 AM
I have used the following

DEFINE donor sele TYPE H* .AND. .BONDED. bynum @IN1 SHOW END
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