Adk44: Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..."

2019-05-13T10:32:33Z

Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..."

New page

Top level: [[CHARMM]]

This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide and computes the energy of the conformation in the crd file.

<pre>
bomblev -2

set molname aladipeptide

! SET PATH to topology and parameter files
! quotes MUST if path has both upper and lower case letters
set pardir "/home/ss2029/svn/CHARMM31/toppar"

! READ TOPOLOGY
open unit 1 read formatted name @pardir/"top_all22_prot.inp"
read rtf card unit 1
close unit 1

! READ PARAMS
open unit 2 read formatted name @pardir/"par_all22_prot.inp"
read para card unit 2
close unit 2

! READ psf from file
open unit 1 form read name @molname.psf
read psf card unit 1
close unit 1

! READ coord from file
open unit 1 card read name @molname.crd
read coor card unit 1
close unit 1

! COMPUTE ENERGY
UPDATE NBOND atom switch cdie vdw vswitch -
ctonnb 979 ctofnb 989 cutnb 999

ENERgy

! end of file
</pre>

Running as

<pre>
$ ~/svn/CHARMM31/exec/gnu/charmm < ener.inp
</pre>

gives the output

<pre>
:
:
CHARMM> ENERgy

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =999.000 CTEXNB =999.000 CTONNB =979.000 CTOFNB =989.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 174 atom pairs and 98 atom exclusions.
There are 0 group pairs and 11 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 221 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
174 ATOM PAIRS WERE FOUND FOR ATOM LIST
0 GROUP PAIRS REQUIRED ATOM SEARCHES

ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ENER> 0 70.55732 0.00000 43.03708
ENER INTERN> 0.02020 28.80010 0.11396 10.08902 51.30174
ENER EXTERN> 5.47894 -25.24663 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

CHARMM>

$$$$$$ New timer profile $$$$$
List time 0.00959 Other: 0.00000
Electrostatic & VDW 0.00004 Other: 0.00000
Nonbond force 0.01572 Other: 0.01568
Bond energy 0.00093 Other: 0.00000
Angle energy 0.00004 Other: 0.00000
Dihedral energy 0.00003 Other: 0.00000
Restraints energy 0.00000 Other: 0.00000
INTRNL energy 0.01781 Other: 0.01682
Energy time 0.04364 Other: 0.01010
Total time 0.43943 Other: 0.38620

NORMAL TERMINATION BY END OF FILE
MAXIMUM STACK SPACE USED IS 47526
STACK CURRENTLY IN USE IS 0
MOST SEVERE WARNING WAS AT LEVEL 1
HEAP PRINTOUT- HEAP SIZE 2048000
SPACE CURRENTLY IN USE IS 172
MAXIMUM SPACE USED IS 2008
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 2047828 NEXT: 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.44 SECONDS
CPU TIME: 0.00 SECONDS
FORTRAN STOP

</pre>

A script for energy minimization is available here /home/ss2029/WORK/DEMOS/CHARMMSCRIPTS/enerMin.inp.

Top level: [[CHARMM]]

--[[User:Ss2029|Ss2029]] 16:18, 22 June 2011 (UTC)

Calculating energy of a conformation - Revision history

Adk44: Created page with "Top level: CHARMM This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide a..."